Tutorial 28: Scripting

Authors: Francois Tadel, Elizabeth Bock, Matthias Sure, Sylvain Baillet

The previous tutorials explained how to use Brainstorm in an interactive way to process one subject with two acquisition runs. In the context of a typical neuroimaging study, you may have tens or hundreds of subjects to process in the same way, it is unrealistic to do everything manually. Some parts of the analysis can be processed in batches with no direct supervision, others require more attention. This tutorial introduces tools and tricks that will help you assemble an efficient analysis pipeline.

Contents

Starting a new script
Line by line: Header
Line by line: Body
Line by line: Footer
Simplify the calls
Evaluate in Matlab
Naming conventions
Running the script
Running the script again
Starting Brainstorm
Database requests
File structures
Custom processing
Reference: File manipulation
Reference: Display functions
Example: Creating a new file
Example: Editing events
Find examples in the code
Additional quality control
Loop over subjects
Loop over acquisition runs
How to process an entire study
Final scripts
Running scripts on a cluster
Finding interface callback functions
Additional documentation

Starting a new script

The easiest way to get started with a new Brainstorm script is to use the script generator, already introduced in the tutorial Select files and run processes. Select some files in the Process1 or Process2 tabs, select a list of processes, and use the menu Generate .m script. The example below should work with the protocol "TutorialIntroduction" created during the introduction tutorials.

In the Process1 tab, leave the selection box empty and click on [Run]. Instead of selecting the files from the Brainstorm interface, we will select them directly from the database using a script.
Select process File > Select files: Recordings (do not execute immediately)
Subject=Subject01, Condition=[Empty], File name=Avg: deviant (the space is important).
This process selects all the recordings with a comment including the string "Avg: deviant", from all the folders in Subject01 (except for "Intra-subject" and "Common files"). We expect to get two files: the averages of the deviant condition for both runs.
Add process Pre-process > Band-pass filter: Lower cutoff=0Hz, Upper cutoff=30Hz, 60dB.
Add process File > Save snapshot: Recordings time series, Sensors=MEG.
This will apply a low-pass filter at 30Hz and save a screen capture of the signals in the report.
Do not run the pipeline, select the menu Generate .m script instead. It saves a new .m file and opens it in the Matlab editor. Close the pipeline editor window and look at the script.
The script you just generated can be the starting point to your own custom script. The following sections explain line by line how they work and how to edit them.

Line by line: Header

% Script generated by Brainstorm (19-Jul-2016)

All the lines starting with a "%" are comments, they are never executed.

% Input files
sFiles = [];
SubjectNames = {...
    'Subject01'};

These lines define the script inputs:

sFiles: The list of files in input. Currently empty because we did not select anything in the Process1 list. If we had selected files, it would contain a cell array of strings with relative file paths.
SubjectNames: List of subject names that are used in the script. Most of the times, the generated scripts contain only one entry, but it is written as a cell array to make it easier to extend to multiple subjects with a loop (described further in this tutorial).

% Start a new report
bst_report('Start', sFiles);

Starts a new report of activity: Clears all the previous logs and gets ready to record new messages. The report will collect all the messages that are generated during the execution of the script by the various processes. You can explicitly add screen captures and additional messages to the current report with the function bst_report. This report will remain open until the function bst_report('Start') is called again. To display the current report, use the menu File > Report viewer.

The syntax function_name('SubFunction', arguments) is used a lot in Brainstorm: it calls a subfunction available inside a .m file. This line above calls the function Start() in the file brainstorm3/toolbox/process/bst_report.m. This is made possible with the use of the short script "macro_method". Many of the Brainstorm .m files are actually libraries of functions, rather than simple "scripts" or "functions".

Line by line: Body

% Process: Select data files in: Subject01/*/Avg: deviant
sFiles = bst_process('CallProcess', 'process_select_files_data', sFiles, [], ...
    'subjectname',   SubjectNames{1}, ...
    'condition',     '', ...
    'tag',           'Avg: deviant', ...
    'includebad',    0, ...
    'includeintra',  0, ...
    'includecommon', 0);

% Process: Low-pass:30Hz
sFiles = bst_process('CallProcess', 'process_bandpass', sFiles, [], ...
    'sensortypes', 'MEG', ...
    'highpass',    0, ...
    'lowpass',     30, ...
    'attenuation', 'strict', ...  % 60dB
    'mirror',      0, ...
    'useold',      0, ...
    'overwrite',   0);

% Process: Snapshot: Recordings time series
sFiles = bst_process('CallProcess', 'process_snapshot', sFiles, [], ...
    'target',         5, ...  % Recordings time series
    'modality',       1, ...  % MEG (All)
    'orient',         4, ...  % bottom
    'time',           0.11, ...
    'contact_time',   [0, 0.1], ...
    'contact_nimage', 12, ...
    'threshold',      20, ...
    'Comment',        'Run');

You will find one block per process you selected in the pipeline editor. They all have the same syntax:
output_files = bst_process('CallProcess', process_name, input_files_A, input_files_B, options_list);

process_name: String indicating the function corresponding to the process to execute. To know from the pipeline editor what is the path to the process function: hover your mouse over the selected process, as illustrated in this tutorial.
input_files_A: List of input files in Process1, or FilesA in Process2. It can be a cell array of file names (full path, or relative path from the protocol folder), or an array of structures describing the files in the database (returned by a previous call to bst_process).
input_files_B: Empty for Process1, or FilesB in Process2. Cell array of strings, or array of struct.
options_list: Pairs of (option_name, option_values), one pair for each option of the process.
output_files: Array of structures describing the files in output of the process. If the process created new files, this variable points at them. If the process didn't create new files or was modifying exiting files, this variable points at the input files.

Line by line: Footer

% Save and display report
ReportFile = bst_report('Save', sFiles);

Closes the current report and saves it in the user report folder ($HOME/.brainstorm/reports). These reports are in .mat format and contain all the information necessary to re-run the execution exactly in the same way, but they are not easy to read.

The parameter "sFiles" is optional, it indicates what are the files that are considered as the final results of the script. You can remove it without breaking your script: ReportFile = bst_report('Save');

bst_report('Open', ReportFile);

Opens the report viewer to display what happened during the execution. This is equivalent to using the menu File > Report viewer. You can comment this line (ie. add a "%" at the beginning of the line) if you don't want to show the report at the end of the execution.

% bst_report('Export', ReportFile, ExportDir);

This function exports the report in readable format, as an HTML file that includes all the screen captures embedded in it. It is disabled by default. If you want to use this feature: remove the "%" at the beginning of the line, and define the variable ExportDir.

ExportDir must be a string that defines where to save the HTML report. It can be either the absolute path to a HTML file (eg. 'C:\Users\myuser\Documents\report_example.html') or just a folder (eg. 'C:\Users\myuser\Documents'). If you enter only a path to a folder, a default file name including the protocol name and a date tag is generated (report_ProtocolName_YYMMDD_HHMMSS.html).

Simplify the calls

The script you generated is like any Matlab script: you can edit it, rename the variables, add tests and loops, etc. The first important thing to understand is how to edit the options and change the inputs/outputs. The script generator uses only one variable for all the file lists (sFiles) and the output process is always the input of the following process. This is usually too restrictive to write a full analysis script: we commonly need to have multiple lists of files or to run two different operations on the same file.

Let's consider the first process call, which selects the averages for the Deviant condition in both runs.

sFiles = bst_process('CallProcess', 'process_select_files_data', sFiles, [], ...
    'subjectname',   SubjectNames{1}, ...
    'condition',     '', ...
    'tag',           'Avg: deviant', ...
    'includebad',    0, ...
    'includeintra',  0, ...
    'includecommon', 0);

There is no need to set the parameter sFiles, because there is no input, you can replace it with an empty matrix []. You can therefore remove the line "sFiles = [];". We can also rename the output variable "sAvgData", to be more specific.

sAvgData = bst_process('CallProcess', 'process_select_files_data', [], [], ...

You can omit all the options that are not defined, not used, or kept to their default values:

sAvgData = bst_process('CallProcess', 'process_select_files_data', [], [], ...
    'subjectname',   SubjectNames{1}, ...
    'tag',           'Avg: deviant');

Edit the call to the low-pass filter: Change the input to sAvgData and the output to sAvgDataLow, this way you will be able to keep track of the two files if you need to use them independently later.

sAvgDataLow = bst_process('CallProcess', 'process_bandpass', sAvgData, [], ...
    'sensortypes', 'MEG', ...
    'highpass',    0, ...
    'lowpass',     30, ...
    'attenuation', 'strict');   % 60dB

Edit the call to the snapshot process: Change the input to sAvgDataLow, and remove the output parameter (we are not expecting any output file from it).

bst_process('CallProcess', 'process_snapshot', sAvgDataLow, [], ...
    'target',   5, ...  % Recordings time series
    'modality', 1);     % MEG (All)

Replace the last lines with the following code, in order to export the report instead of opening in the report viewer (edit the file path to point at your own user folder instead).

ReportFile = bst_report('Save');
bst_report('Export', ReportFile, 'C:\Users\myuser\Documents\report_test.html');

Evaluate in Matlab

Select the code for the first process in the Matlab editor, right-click > Evaluate selection (or press F9).

If you haven't executed your script yet, you will get the following error in the Matlab command window:

Undefined variable "SubjectNames" or class "SubjectNames".

The variable SubjectNames is not defined yet: Execute the first lines "SubjectNames = {'Subject01'}", then try again. You should now have a new variable in your Matlab workspace, which points at the two average files. Type "sAvgData(1)" in your command window to display the first element:

>> sAvgData(1)
ans =
          iStudy: 6
           iItem: 1
        FileName: '..._01_600Hz_notch/data_deviant_average_160513_1329.mat'
        FileType: 'data'
         Comment: 'Avg: deviant (39 files)'
       Condition: 'S01_AEF_20131218_01_600Hz_notch'
     SubjectFile: 'Subject01/brainstormsubject.mat'
     SubjectName: 'Subject01'
        DataFile: ''
     ChannelFile: 'Subject01/S01_AEF_20131218_01_600Hz_notch/channel_ctf_acc1.mat'
    ChannelTypes: {'ADC A'  'ADC V'  'DAC'  'ECG'  'EOG'  'MEG'  'MEG REF' ...}

The field "sAvgData(1).FileName" contains the relative path to the to the Deviant average in the first run. This structure sAvgData contains also a lot of information that can be helpful in your script:

iStudy / iItem: Reference of the file in the database (described later in this tutorial).
FileType: 'raw' (continuous files), 'data' (recordings), 'results' (sources), 'timefreq' (time-frequency, spectrum and connectivity), or 'matrix' (any time series extracted from other files).
Comment: Comment/Name field of the file (what is displayed in the database explorer).
Condition: Name of the condition/folder in which the file is located.
SubjectFile: Relative path to the subject file (brainstormsubject.mat).
SubjectName: Name of the subject (must be the same as the folder name).
DataFile: For types 'results' or 'timefreq', path of the parent file in the database explorer.
ChannelFile: Relative path to the channel file.
ChannelTypes: Cell array of channel types available for the input file.

Naming conventions

To help you navigate in the Brainstorm code, here are some naming conventions:

Structures: Name starting with a "s" followed by a capital letter (eg. sFiles, sStudy, sSubject).
Indices: Either loop variables or array indices, name starting with a "i" (eg. iSubject, iStudy, iTime).
Counts: Number of elements in a group, name starting with a "n" (eg. nAvg, nTrials, nSubjects).
Graphic handles: Matlab graphic objects, name starting with a "h" (eg. hFig, hAxes, hLine, hText).
File names: Scripts and functions, only lower case, separation with "_" (eg. process_fft, bst_get).
Sub-functions: Inside a .m file, name starting with a capital, CamelCase (eg. CallProcess, Start).

Running the script

The simplified script looks like this:

% Input files
SubjectNames = {'Subject01'};
% Start a new report
bst_report('Start');

% Process: Select data files in: Subject01/*/Avg: deviant
sAvgData = bst_process('CallProcess', 'process_select_files_data', [], [], ...
    'subjectname',   SubjectNames{1}, ...
    'tag',           'Avg: deviant');
% Process: Low-pass:30Hz
sAvgDataLow = bst_process('CallProcess', 'process_bandpass', sAvgData, [], ...
    'sensortypes', 'MEG', ...
    'highpass',    0, ...
    'lowpass',     30, ...
    'attenuation', 'strict');  % 60dB
% Process: Snapshot: Recordings time series
bst_process('CallProcess', 'process_snapshot', sAvgDataLow, [], ...
    'target',   5, ...  % Recordings time series
    'modality', 1);     % MEG (All)

% Save and display report
ReportFile = bst_report('Save');
bst_report('Export', ReportFile, 'C:\Users\franc\Documents\report_test.html');

You have three ways to execute it:

Select all the lines (Ctrl+A) and evaluate it in Matlab (F9).
In the Editor toolbar of the Matlab environment, click on the button [Run].
Save the file, go to this folder with Matlab (or add it to your path) and type the name of the script in the command window (without the ".m" at the end).

At the end of the execution, nothing happens, because we indicated we wanted to export the report instead of opening it. To check out the report of execution: use the menu File > Report viewer from the Brainstorm window, or open the file report_test.html that was saved somewhere on your computer.

In this page, you can review everything that happened in the script: when it was executed, how long it took, what are the processes that were executed, some additional messages (two files were selected with the first process) and the screen captures taken by process_snapshot.

Running the script again

If you execute the script again, it will not behave as expected anymore. The selection process we used assumes that there is only one file per folder with a name that includes "Avg: deviant". This is not the case anymore after the execution, because the low-pass filtered files also contain the same string. The execution of the first process of the script now returns 4 files.

>> sAvgData = bst_process('CallProcess', 'process_select_files_data', [], [], ...
    'subjectname',   SubjectNames{1}, ...
    'tag',           'Avg: deviant')

sAvgData =
1x4 struct array with fields:
    iStudy
    iItem
    ...

In order to exclude the low-pass filtered files from this selection, you can add another process that will refine the selection. Use the script generator again to create a template call for another process, then copy-paste it in your script.

In Process1: Select any recordings file (we will not run anything, just generate a script).
Select process File > Select files: By tag: Search="low", Search the file name, Ignore the files.
Select the menu Generate .m script (make sure you do not overwrite the script you are currently working on), then close the pipeline editor.
Copy-paste and edit the call to process_select_tag to your main script.

Now the file selection part of your script should look like this, and should return only two files:

% Process: Select data files in: Subject01/*/Avg: Deviant
sAvgData = bst_process('CallProcess', 'process_select_files_data', [], [], ...
    'subjectname',   SubjectNames{1}, ...
    'tag',           'Avg: deviant');
% Process: Ignore file names with tag: low
sAvgData = bst_process('CallProcess', 'process_select_tag', sAvgData, [], ...
    'tag',    'low', ...
    'search', 2, ...  % Search the file names
    'select', 2);  % Ignore the files with the tag

With this last modification, your script is more robust. It can be executed multiple times without completely changing its behavior. When you are fetching files from the database using tags or file names, always pay attention to this aspect: the database grows and the further you go, the more specific your requests have to be.

A good practice can be to tag explicitly the output files your script generates if you need to fetch them later. You can use the process File > Add tag and File > Set name.

Starting Brainstorm

Brainstorm must be running in the background for these scripts to run properly. The interface doesn't have to be visible on the screen, but the database engine must be running for processing requests. At the beginning of your script, you can explicitly start or restart Brainstorm.

brainstorm: Start Brainstorm with the regular GUI.
brainstorm nogui: Start in silent mode. The Java GUI is created but hidden, the progress bar is not shown, all the processes run without user interactions, using default options instead of asking interactively. Visualization figures opened in the processing scripts are still created and made visible.
brainstorm server: Start in headless mode, for execution on a distant computation server that does not have any graphical capability or display attached to it. In this mode, none of the Java GUI elements are created, and the Matlab figures are not displayed. Whether you would be able to add screen captures to your execution reports depends mostly on the Matlab version available of your server (see section below Running scripts on a cluster).
brainstorm <script.m> <parameters>: Start Brainstorm in server mode, execute a script and quit Brainstorm. This allows executing any Matlab or Brainstorm script from the command line. This works also from the compiled version of Brainstorm, executed with the free MATLAB Runtime (see installation instructions, section "without Matlab"). Add the full path to the script and parameters to the command line:
- Windows: brainstorm3.bat <script.m> <parameters>
- Linux/MacOS: brainstorm3.command <MATLABROOT> <script.m> <parameters>
  MATLABROOT: Matlab Runtime installation folder, eg. /usr/local/MATLAB_Runtime/v98/
brainstorm ... local: Instead of using a user defined brainstorm_db folder, it would use the default folder for the database: $HOME/.brainstorm/local_db

If you want to start Brainstorm only if it is not already running, you can use the following code:

if ~brainstorm('status')
    brainstorm nogui
end

To select a specific protocol at the beginning of your script:

ProtocolName = 'TutorialIntroduction';
% Get the protocol index
iProtocol = bst_get('Protocol', ProtocolName);
if isempty(iProtocol)
    error(['Unknown protocol: ' ProtocolName]);
end
% Select the current procotol
gui_brainstorm('SetCurrentProtocol', iProtocol);

To delete the protocol and start over:

% Delete existing protocol
gui_brainstorm('DeleteProtocol', ProtocolName);
% Create new protocol
gui_brainstorm('CreateProtocol', ProtocolName, 0, 0);

Additional command line options:

brainstorm stop      % Quit Brainstorm
brainstorm update    % Download and install latest Brainstorm update (see bst_update)
brainstorm reset     % Re-initialize Brainstorm database and preferences
brainstorm digitize  % Digitize electrodes positions and head shape using a Polhemus
brainstorm setpath   % Add Brainstorm subdirectories to current path
brainstorm info      % Open Brainstorm website
brainstorm forum     % Open Brainstorm forum
brainstorm license   % Display license

Database requests

The functions bst_get and bst_set allow you to query the database, access the configuration of the software and modify some display parameters. The complete reference documentation of these functions is included directly in their code (brainstorm3/toolbox/core/bst_get.m and bst_set.m).

Let's start with a few simple examples:

>> ProtocolInfo = bst_get('ProtocolInfo')  % Configuration of the current protocol
ProtocolInfo =
              Comment: 'TutorialIntroduction'
              STUDIES: 'C:\Work\Protocols\TutorialIntroduction\data'
             SUBJECTS: 'C:\Work\Protocols\TutorialIntroduction\anat'
               iStudy: 6
       UseDefaultAnat: 0
    UseDefaultChannel: 0

>> isGUI = bst_get('isGUI')   % Is the Brainstorm interface displayed (0=no, 1=yes)

>> bst_set('FlipYAxis', 1)                 % New figures will have the Y axis flipped
>> bst_set('TSDisplayMode', 'butterfly')   % New figures will use a "butterfly" view

To reference the files in the database, each protocol is subdivided in Subjects (the "anat" folder, containing the MRI, surfaces and atlases) and Studies (the "data" folder, including the recordings, channel files and all the analyses). Each Study corresponds to a sub-folder (eg. protocol/data/subject01/run01/), and is attached to only one subject.

Subjects and Studies are referenced in the protocol with a unique index, most of the time kept in variables named iSubject and iStudy. The files available in them are also referenced with indices, with variables such as iAnatomy, iSurface, iData, iHeadModel, iResults or iTimefreq. You can see the indices in the database explorer by hovering your mouse over the nodes files and folders:

Example: Getting the study structure from the variable sAvgData, defined in the script:

>> sAvgData(1)
ans =
          iStudy: 6
           iItem: 1
           ...

>> sStudy = bst_get('Study', sAvgData(1).iStudy)   % Get study struct with its index
sStudy =
                 Name: 'S01_AEF_20131218_01_600Hz_notch'
             FileName: 'Subject01/S01_AEF_20131218_01_600Hz_notch/brainstormstudy.mat'
          DateOfStudy: '13-May-2016'
    BrainStormSubject: 'Subject01/brainstormsubject.mat'   % Subject filename
            Condition: {'S01_AEF_20131218_01_600Hz_notch'} % Name of the folder
              Channel: [1x1 struct]       % Channel file
             iChannel: []                 % Not used anymore
                 Data: [1x242 struct]     % List of "data" files in the folder
            HeadModel: [1x1 struct]       % List of head models in the folder
           iHeadModel: 1                  % Default head model (file in green)
               Result: [1x244 struct]     % List of source files and links
                 Stat: [1x0 struct]       % List of statistical results
                Image: [0x0 struct]       % List of images
             NoiseCov: [1x2 struct]       % Noise(1) and data(2) covariance files
              Dipoles: [0x0 struct]       % List of dipole files in the folder
             Timefreq: [1x247 struct]     % List of time-frequency files
               Matrix: [0x0 struct]       % List of "matrix" files in the folder

Example: Getting the data structure.

% Get the structure representing the file from sStudy
>> sData = sStudy.Data(sAvgData(1).iItem)
sData =
    FileName: '..._01_600Hz_notch/data_deviant_average_160513_1329.mat'
     Comment: 'Avg: deviant (39 files)'    % File name
    DataType: 'recordings'                 % Type of data in the file
    BadTrial: 0                            % If 1, the trial is marked as bad

Example: Getting the subject structure.

% Get subject structure from filename (lists the files in the subject folder)
>> sSubject = bst_get('Subject', sStudy.BrainStormSubject)
sSubject =
                 Name: 'Subject01'    % Subject name, same as folder name
             Comments: ''             % Not used much
             FileName: 'Subject01/brainstormsubject.mat'
    DateOfAcquisition: ''             % Not used anymore
              Anatomy: [1x1 struct]   % List of MRI volumes
              Surface: [1x9 struct]   % List of surfaces
             iAnatomy: 1              % Index of default MRI
               iScalp: 9              % Index of default head surface
              iCortex: 4              % Index of default cortex surface
          iInnerSkull: []             % Index of default inner skull surface
          iOuterSkull: []             % Index of default outer skull surface
               iOther: []             % Not used anymore
       UseDefaultAnat: 0        % If 1: Use the default anatomy
    UseDefaultChannel: 0        % 0=one/folder, 1=one/subject, 2=one global

Example: Getting the study structure and data index from a file name.

>> DataFile = sAvgData(1).FileName
DataFile =
Subject01/..._01_600Hz_notch/data_deviant_average_160513_1329.mat

>> [sStudy, iStudy, iData] = bst_get('DataFile', DataFile)
sStudy =
                 Name: 'S01_AEF_20131218_01_600Hz_notch'
             FileName: '..._01_600Hz_notch/brainstormstudy.mat'
          DateOfStudy: '13-May-2016'
    BrainStormSubject: 'Subject01/brainstormsubject.mat'
            Condition: {'S01_AEF_20131218_01_600Hz_notch'}
              Channel: [1x1 struct]
             iChannel: []
                 Data: [1x242 struct]
            HeadModel: [1x1 struct]
           iHeadModel: 1
               Result: [1x244 struct]
                 Stat: [1x0 struct]
                Image: [0x0 struct]
             NoiseCov: [1x2 struct]
              Dipoles: [0x0 struct]
             Timefreq: [1x247 struct]
               Matrix: [0x0 struct]
iStudy =
     6
iData =
     1

Many other options are available for searching files in the database with bst_get. We cannot list them all in this page, but you can refer to the code of bst_get.m for more information.

function [argout1, argout2, argout3, argout4, argout5] = bst_get( varargin )
% BST_GET: Get a Brainstorm structure.
% This function is used to abstract the way that these structures are stored.
%
% USAGE :
% ====== DIRECTORIES ==================================================================
%    - bst_get('UserDir')               : User home directory
%    - bst_get('BrainstormHomeDir')     : Application directory of brainstorm
%    - bst_get('BrainstormUserDir')     : User home directory for brainstorm (<home>/.brainstorm/)
%    - bst_get('BrainstormTmpDir')      : User brainstorm temporary directory (Default: <home>/.brainstorm/tmp/)
%    - bst_get('BrainstormTmpDir', isForcedDefault)   : User DEFAULT brainstorm temporary directory (<home>/.brainstorm/tmp/)
%    - bst_get('BrainstormDocDir')      : Doc folder folder of the Brainstorm distribution (may vary in compiled versions)
%    - bst_get('BrainstormDefaultsDir') : Defaults folder folder of the Brainstorm distribution (may vary in compiled versions)
%    - bst_get('BrainstormPluginDir')   : User home directory for brainstorm (<home>/.brainstorm/)
%    - bst_get('UserReportsDir')        : User reports directory (<home>/.brainstorm/reports/)
%    - bst_get('UserMexDir')            : User temporary directory (<home>/.brainstorm/mex/)
%    - bst_get('UserProcessDir')        : User custom processes directory (<home>/.brainstorm/process/)
%    - bst_get('UserDefaultsDir')       : User defaults directory (<home>/.brainstorm/defaults/)
%    - bst_get('UserPluginsDir')        : User plugins directory (<home>/.brainstorm/plugins/)
%    - bst_get('BrainstormDbFile')      : User brainstorm.mat file (<home>/.brainstorm/brainstorm.mat)
%    - bst_get('BrainstormDbDir')       : User database directory (contains all the brainstorm protocols)
%    - bst_get('DirDefaultSubject')     : Directory name of the default subject
%    - bst_get('DirDefaultStudy')       : Directory name of the default study for each subject
%    - bst_get('DirAnalysisInter')      : Directory name of the inter-subject analysis study 
%    - bst_get('DirAnalysisIntra')      : Directory name of the intra-subject analysis study (for each subject)
%    - bst_get('AnatomyDefaults')       : Get the contents of directory bstDir/defaults/anatomy
%    - bst_get('MniAtlasDefaults')      : Get the contents of directory bstDir/defaults/mniatlas
%    - bst_get('EegDefaults')           : Get the contents of directory bstDir/defaults/eeg
%    - bst_get('LastUsedDirs')          : Structure with all the last used directories (last used)
%    - bst_get('OsType', isMatlab=1)    : Get a string that describes the operating system (if isMatlab=1 return the Matlab/JVM platform, else return the real host system)
%    - bst_get('FileFilters', DataType) : Get the list of import filters for a specific data type
%    - bst_get('PluginCustomPath')      : Full custom path to all plugins
%    - bst_get('BrainSuiteDir')         : Full path to a local installation of BrainSuite
%    - bst_get('SpmTpmAtlas')           : Full path to the SPM atlas TPM.nii
%    - bst_get('PythonExe')             : Path to the python executable
%
% ====== PROTOCOLS ====================================================================
%    - bst_get('iProtocol')             : Indice of current protocol 
%    - bst_get('Protocol', ProtocolName): Return the indice of the protocol ProtocolName, or [] if it doesn't exist
%    - bst_get('ProtocolInfo')          : Definition structure for current protocol
%    - bst_get('ProtocolSubjects')      : Subjects list for current protocol
%    - bst_get('ProtocolStudies')       : Studies list for current protocol
%    - bst_get('isProtocolLoaded')      : 1 if the protocol has been loaded, 0 else
%    - bst_get('isProtocolModified')    : 1 if the protocol has been modified, 0 else
%
% ====== STUDIES ======================================================================
%    - bst_get('Study', StudyFileName)  : Get one study in current protocol with its file name
%    - bst_get('Study', iStudies)       : Get one or more studies
%    - bst_get('Study')                 : Get current study in current protocol
%    - bst_get('StudyCount')            : Get number of studies in the current protocol
%    - bst_get('StudyWithSubject',   SubjectFile)          : Find studies associated with a given subject file (WITHOUT the system studies ('intra_subject', 'default_study'))
%    - bst_get('StudyWithSubject',   ..., 'intra_subject') : Find studies ... INCLUDING 'intra_subject' study
%    - bst_get('StudyWithSubject',   ..., 'default_study') : Find studies ... INCLUDING 'default_study' study
%    - bst_get('StudyWithCondition', ConditionPath)        : Find studies for a given condition path
%    - bst_get('ChannelStudiesWithSubject', iSubjects)     : Get all the studies where there should be a channel file for a list of subjects
%    - bst_get('AnalysisIntraStudy', iSubject)    : Get the default analysis study for target subject
%    - bst_get('AnalysisInterStudy')              : Get the default analysis study for inter-subject analysis
%    - bst_get('DefaultStudy', iSubject)          : Get the default study for target subject (by subject indice)
%    - bst_get('DefaultStudy')                    : Get the global default study (common to all subjects)
%    - bst_get('DefaultStudy', SubjectFile)       : Get the default study for target subject (by filename)
%    - bst_get('ChannelFile', ChannelFile)        : Find a channel file in current protocol
%    - bst_get('ChannelFileForStudy', StudyFile/DataFile)  : Find a channel file in current protocol
%    - bst_get('ChannelForStudy',   iStudies)     : Return current Channel struct for target study
%    - bst_get('ChannelModalities', ChannelFile)  : Return displayable modalities for a Channel file
%    - bst_get('ChannelModalities', DataFile)     : Return displayable modalities for a Data/Results/Timefreq... file
%    - bst_get('ChannelDevice', ChannelFile)      : Return acquisistion device for a channel file
%    - bst_get('TimefreqDisplayModalities', TfFile)     : Get displayable modalities for a TF file based on recordings
%    - bst_get('HeadModelForStudy',   iStudy)           : Return current HeadModel struct for target study
%    - bst_get('HeadModelFile', HeadModelFile)          : Find a HeadModel file in current protocol
%    - bst_get('HeadModelFile', HeadModelFile, iStudies): Find a HeadModel file in current protocol
%    - bst_get('NoiseCovFile', NoiseCovFile)            : Find a noise covariance file file in current protocol
%    - bst_get('NoiseCovFile', NoiseCovFile, iStudies)  : Find a noise covariance file in current protocol
%    - bst_get('NoiseCovFile', DataCovFile)             : Find a data covariance file file in current protocol
%    - bst_get('NoiseCovFile', DataCovFile, iStudies)   : Find a data covariance file file in current protocol
%    - bst_get('DataFile',    DataFile)                 : Find a DataFile in current protocol
%    - bst_get('DataFile',    DataFile, iStudies)       : Find a DataFile in current protocol
%    - bst_get('DataForDataList', iStudy, DataListName) : Find all the DataFiles grouped by a data list
%    - bst_get('DataForStudy', iStudy)                  : Find all the Data files that are dependent on the channel/headmodel of a given study
%    - bst_get('DataForStudies', iStudies)
%    - bst_get('DataForChannelFile', ChannelFile)       : Find all the DataFiles that use the given ChannelFile
%    - bst_get('ResultsFile', ResultsFile)              : Find a ResultsFile in current protocol
%    - bst_get('ResultsFile', ResultsFile, iStudies)    : Find a ResultsFile in input studies
%    - bst_get('ResultsForDataFile', DataFile, iStudies): Find all results computed based on DataFile
%    - bst_get('StatFile', StatFile)                    : Find a StatFile in current protocol
%    - bst_get('StatFile', StatFile, iStudies)          : Find a StatFile in input studies
%    - bst_get('StatForDataFile',   DataFile, iStudies)
%    - bst_get('StatForDataFile',   DataFile)
%    - bst_get('TimefreqFile',      TimefreqFile)
%    - bst_get('TimefreqFile',      TimefreqFile, iStudies)
%    - bst_get('TimefreqForFile',   FileName, iStudies)   : Find all timefreq files computed based on target file
%    - bst_get('TimefreqForKernel', KernelFile) 
%    - bst_get('DipolesFile',       DipolesFile)
%    - bst_get('DipolesFile',       DipolesFile, iStudies)
%    - bst_get('DipolesForFile',    FileName, iStudies)   : Find all dipoles files computed based on target file
%    - bst_get('DipolesForKernel',  KernelFile) 
%    - bst_get('MatrixFile',        MatrixFile)
%    - bst_get('MatrixFile',        MatrixFile, iStudies)
%    - bst_get('MatrixForMatrixList', iStudy, MatrixListName)
%    - bst_get('AnyFile',           AnyFile)
%    - bst_get('AnyFile',           AnyFile, iStudies)
%    - bst_get('RelatedDataFile',   FileName)
%    - bst_get('RelatedDataFile',   FileName, iStudies)
%    - bst_get('GetFilenames')
%
% ====== SUBJECTS ======================================================================
%    - bst_get('Subject', SubjectFileName, isRaw) : Find a subject in current protocol with its file name
%    - bst_get('Subject', SubjectName, isRaw)     : Find a subject in current protocol with its name
%    - bst_get('Subject', iSubject)               : Get a subject (normal or default if iSubject==0)
%    - bst_get('Subject')                         : Get current subject in current protocol
%    - bst_get('SubjectCount')                    : Get number of studies in the current protocol
%    - bst_get('NormalizedSubjectName')           : Name of the subject with a normalized anatomy
%    - bst_get('NormalizedSubject')               : Get groupd analysis subject for the current protocol
%    - bst_get('ConditionsForSubject', SubjectFile)           : Find all conditions for a given subject
%    - bst_get('SurfaceFile',          SurfaceFile)           : Find a surface in current protocol
%    - bst_get('SurfaceFileByType',    iSubject,    SurfaceType) : Find surfaces with given type for subject #i (default only)
%    - bst_get('SurfaceFileByType',    SubjectFile, SurfaceType) : Find surfaces with given type for subject SubjectFile (default only)
%    - bst_get('SurfaceFileByType',    SurfaceName, SurfaceType) : Find surfaces with given type for subject that also has surface SurfaceName (default only)
%    - bst_get('SurfaceFileByType',    MriName,     SurfaceType) : Find surfaces with given type for subject that also has MRI MriName  (default only)
%    - bst_get('SurfaceFileByType',    ...,  ..., isDefaultOnly) : If 0, return all the surfaces of the given type, instead of only the default surface
%    - bst_get('MriFile',              MriFile)               : Find a MRI in current protocol
% 
% ====== GUI =================================================================
%    - bst_get('BstControls')    : Return main Brainstorm GUI structure
%    - bst_get('BstFrame')       : Return main Brainstorm JFrame
%    - bst_get('isGUI')          : Return 1 if the Brainstorm interface is displayed
%    - bst_get('GuiLevel')       : Return GUI level:  -1=server, 0=nogui, 1=normal, 2=autopilot
%    - bst_get('ScreenDef')      : Get screens configuration
%    - bst_get('DecorationSize') : Get dimensions of the windows decorations
%    - bst_get('Layout')         : Configuration of the main Brainstorm window
%    - bst_get('Layout', prop)   : Get one property in the layout properties
%    - bst_get('PanelContainer')                : Display list of registered panel containers
%    - bst_get('PanelContainer', ContainerName) : Get a panel container handle
%    - bst_get('Panel')                         : Display list of registered panels
%    - bst_get('Panel',         PanelName)      : Find a panel with its name
%    - bst_get('PanelControls', PanelName)      : Get the controls of a panel
%    - bst_get('Clipboard')       : Nodes that were copied from the interface
%    - bst_get('FigFont')         : Standard font size displayed in the figures
%    - bst_get('Font')            : Create a Java font, scaled for the operating system
%
% ====== CONFIGURATION =================================================================
%    - bst_get('Version')               : Brainstorm version
%    - bst_get('MatlabVersion')         : Matlab version (version number * 100, eg. 801)
%    - bst_get('MatlabReleaseName')     : Matlab version (release name, eg. "R2014a")
%    - bst_get('JavaVersion')           : Java version
%    - bst_get('isJavacomponent')       : Returns 1 if javacomponent is available (Matlab < 2019b), 0 otherwise
%    - bst_get('SystemMemory')          : Amount of memory available, in Mb
%    - bst_get('ByteOrder')             : {'l','b'} - Byte order used to read and save binary files 
%    - bst_get('TSDisplayMode')         : {'butterfly','column'}
%    - bst_get('ElectrodeConfig', Modality)  : Structure describing the current display values for SEEG/ECOG/EEG contacts
%    - bst_get('AutoUpdates')                : {0,1} - If 1, check automatically for updates at startup
%    - bst_get('ForceMatCompression')   : {0,1} - If 1, always save mat-files using the v7 format instead of v6
%    - bst_get('IgnoreMemoryWarnings')  : {0,1} - If 1, do not display memory warnings at the Brainstorm startup
%    - bst_get('ExpertMode')            : {0,1} - If 1, show advanced options that regular user do not see
%    - bst_get('DisplayGFP')            : {0,1} - If 1, the GFP is displayed on all the time series figures
%    - bst_get('DownsampleTimeSeries')  : {0,1,...} - If > 0, downsample dense time series for faster display
%    - bst_get('DisableOpenGL')         : {0,1,2} - If 1, do not use OpenGL renderer; if 2, use software OpenGL
%    - bst_get('InterfaceScaling')      : {100,125,150,...} - Scales the Brainstorm GUI by a fixed factor
%    - bst_get('GraphicsSmoothing')     : {0,1} - If 1, uses the graphics smoothing (Matlab >= 2014b)
%    - bst_get('SystemCopy')            : {0,1} - If 1, uses the system calls mv/cp instead of movefile/copyfile (Linux only)
%    - bst_get('JOGLVersion')           : {0,1,2}, Detect the current version of JOGL available in Matlab
%    - bst_get('DefaultFormats')        : Default formats for importing/exporting data, channels, ... (last used)
%    - bst_get('BFSProperties')         : Conductivities and thicknesses for 3-shell spherical forward model
%    - bst_get('ImportDataOptions')     : Import options for recordings
%    - bst_get('ImportEegRawOptions')   : Importation options for RAW EEG format
%    - bst_get('BugReportOptions')      : Bug reporter options
%    - bst_get('DefaultSurfaceDisplay') : Default display options for surfaces (smooth, data threshold, sulci map)
%    - bst_get('MagneticExtrapOptions') : Structure with the options for magnetic field extrapolation
%    - bst_get('DefaultFreqBands')
%    - bst_get('TimefreqOptions_morlet')
%    - bst_get('TimefreqOptions_fft')
%    - bst_get('TimefreqOptions_psd')
%    - bst_get('TimefreqOptions_hilbert')
%    - bst_get('OpenMEEGOptions')
%    - bst_get('DuneuroOptions')
%    - bst_get('GridOptions_headmodel')
%    - bst_get('GridOptions_dipfit')
%    - bst_get('UniformizeTimeSeriesScales') : {0,1} - If 1, the Y-axis of all the time series figures have the scale
%    - bst_get('FlipYAxis')                  : {0,1} - If 1, the recordings are displayed with the negative values UP
%    - bst_get('AutoScaleY')                 : {0,1} - If 1, the axis limits are updated when the figure is updated
%    - bst_get('ShowXGrid')                  : {0,1} - If 1, show the XGrid in the time series figures
%    - bst_get('ShowYGrid')                  : {0,1} - If 1, show the YGrid in the time series figures
%    - bst_get('ShowZeroLines')              : {0,1} - If 1, show the Y=0 lines in the columns view
%    - bst_get('ShowEventsMode')             : {'dot','line','none'}
%    - bst_get('Resolution')                 : [resX,resY] fixed resolutions for X and Y axes
%    - bst_get('FixedScaleY', Modality)      : Struct with the scales to impose on the recordings for the selected modality
%    - bst_get('XScale', XScale)             : {'log', 'linear'}
%    - bst_get('YScale', YScale)             : {'log', 'linear'}
%    - bst_get('UseSigProcToolbox')       : Use Matlab's Signal Processing Toolbox when available
%    - bst_get('RawViewerOptions', sFile) : Display options for RAW recordings, adapt for specific file
%    - bst_get('RawViewerOptions')        : Display options for RAW recordings
%    - bst_get('TopoLayoutOptions')       : Display options for 2DLayout display
%    - bst_get('StatThreshOptions')       : Options for online statistical thresholding
%    - bst_get('ContactSheetOptions')     : Display options for contact sheets
%    - bst_get('ProcessOptions')          : Options related with the data processing
%    - bst_get('CustomColormaps')         : Gets the list of user defined colormaps
%    - bst_get('MriOptions')              : Configuration for MRI display
%    - bst_get('DigitizeOptions')         : Digitizer options
%    - bst_get('ReadOnly')                : Read only interface
%    - bst_get('NodelistOptions')         : Structure with the options for file selection in the Process1 and Process2 panels
%    - bst_get('ResizeFunction')          : Get the appropriate resize function
%    - bst_get('groot')                   : Get the root graphic object
%    - bst_get('JFrame', hFig)            : Get the underlying java frame for a Matlab figure
%    - bst_get('LastPsdDisplayFunction')  : Display option of measure for spectrum (log, power, magnitude, etc.)
%    - bst_get('PlotlyCredentials')       : Get the credentials and URL to connect to plot.ly server
%    - bst_get('ExportBidsOptions')       : Additional metadata for BIDS export
%
% SEE ALSO bst_set

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
% 
% Copyright (c)2000-2020 University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
% 
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
%
% For more information type "brainstorm license" at command prompt.
% =============================================================================@
%
% Authors: Francois Tadel, 2008-2021
%          Martin Cousineau, 2017

%% ==== PARSE INPUTS ====
global GlobalData;
if ((nargin >= 1) && ischar(varargin{1}))
    contextName = varargin{1};
else
    return
end
% Initialize returned variable
argout1 = [];
argout2 = [];
argout3 = [];
argout4 = [];
argout5 = [];

% Get required context structure
switch contextName
%% ==== SUBFUNCTIONS =====
    case 'findFileInStudies'
        [argout1, argout2, argout3] = findFileInStudies(varargin{2:end});
        
%% ==== BRAINSTORM CONFIGURATION ====
    case 'Version'
        argout1 = GlobalData.Program.Version;
        
    case 'MatlabVersion'
        if ~exist('version','builtin')
            Version = 601;
        else
            % Get version number
            str_vers = version();
            vers = sscanf(str_vers, '%d.%d%*s');
            if isempty(vers) || any(~isnumeric(vers)) || any(isnan(vers))
                vers = 0;
            end
            Version = 100 * vers(1) + vers(2);
            % Get release name
            ipar = [find(str_vers == '('), find(str_vers == ')')];
        end
        argout1 = Version;
        
    case 'MatlabReleaseName'
        if ~exist('version','builtin')
            Release = 'Matlab6';
        else
            % Get version number
            str_vers = version();
            % Get release name
            ipar = [find(str_vers == '('), find(str_vers == ')')];
            Release = str_vers(ipar(1)+1:ipar(2)-1);
        end
        argout1 = Release;

    case 'JavaVersion'
        strver = char(java.lang.System.getProperty('java.version'));
        iDot = find(strver == '.');
        if (length(iDot) < 2)
            argout1 = str2num(strver);
        else 
            argout1 = str2num(strver(1:iDot(2)-1));
        end
        
    case 'isJavacomponent'
        % After Matlab 2019b, javacomponent() and JavaFrame property have been deprecated
        argout1 = (bst_get('MatlabVersion') <= 906);
        
    case 'SystemMemory'
        maxvar = [];
        totalmem = [];
        if ispc && (bst_get('MatlabVersion') >= 706)
            try
                % Get memory info
                usermem  = memory();
                maxvar   = round(usermem.MaxPossibleArrayBytes / 1024 / 1024);
                totalmem = round(usermem.MemAvailableAllArrays / 1024 / 1024);
            catch
                % Whatever...
            end
        end
        argout1 = maxvar;
        argout2 = totalmem;
            
    case 'BrainstormHomeDir'
        argout1 = GlobalData.Program.BrainstormHomeDir;
    case 'BrainstormDbDir'
        argout1 = GlobalData.DataBase.BrainstormDbDir;
    case 'UserDir'
        try
            if ispc
                userDir = getenv('USERPROFILE');
            else
                userDir = char(java.lang.System.getProperty('user.home'));
            end
        catch
            userDir = '';
        end
        if isempty(userDir)
            userDir = bst_get('BrainstormHomeDir');
        end
        argout1 = userDir;
        
    case 'BrainstormUserDir'
        bstUserDir = bst_fullfile(bst_get('UserDir'), '.brainstorm');
        if ~isdir(bstUserDir)
            res = mkdir(bstUserDir);
            if ~res
                error(['Cannot create Brainstorm user directory: "' bstUserDir '".']); 
            end
        end
        argout1 = bstUserDir;
        
    case 'BrainstormTmpDir'
        tmpDir = '';
        isForcedDefault = ((nargin >= 2) && varargin{2});
        % Default folder: userdir/tmp
        defDir = bst_fullfile(bst_get('BrainstormUserDir'), 'tmp');
        % If temporary directory is set in the preferences
        if ~isForcedDefault && isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'BrainstormTmpDir')
            tmpDir = GlobalData.Preferences.BrainstormTmpDir;
        end 
        % Else: use directory userdir/tmp
        if isempty(tmpDir)
            tmpDir = defDir;
        end
        % Create directory if it does not exist yet
        if ~isdir(tmpDir)
            res = mkdir(tmpDir);
            if ~res && ~strcmp(tmpDir, defDir)
                disp(['BST> Cannot create Brainstorm temporary directory: "' tmpDir '".']); 
                disp(['BST> Using default directory instead: "' defDir '".']);
                % Create temporary folder
                tmpDir = defDir;
                if ~isdir(tmpDir)
                    res = mkdir(tmpDir);
                else
                    res = 1;
                end
            end
            % Error: cannot create any temporary folder
            if ~res
                error(['Cannot create Brainstorm temporary directory: "' tmpDir '".']); 
            end
        end
        argout1 = tmpDir;
        
    case 'BrainstormDocDir'
        docDir = bst_fullfile(GlobalData.Program.BrainstormHomeDir, 'doc');
        if ~exist(docDir, 'file')
            % Matlab compiler >= 2018b stores 'doc' under 'bst_javabuil'
            docDir = bst_fullfile(GlobalData.Program.BrainstormHomeDir, 'bst_javabuil', 'doc');
            if ~exist(docDir, 'file')
                docDir = '';
                disp('BST> Could not find "doc" folder.');
                disp(['BST> BrainstormHomeDir = ' GlobalData.Program.BrainstormHomeDir]);
            end
        end
        argout1 = docDir;

    case 'BrainstormDefaultsDir'
        defaultsDir = bst_fullfile(GlobalData.Program.BrainstormHomeDir, 'defaults');
        if ~exist(defaultsDir, 'file')
            % Matlab compiler >= 2018b stores 'defaults' under 'bst_javabuil'
            defaultsDir = bst_fullfile(GlobalData.Program.BrainstormHomeDir, 'bst_javabuil', 'defaults');
            if ~exist(defaultsDir, 'file')
                defaultsDir = '';
                disp('BST> Could not find "defaults" folder.');
                disp(['BST> BrainstormHomeDir = ' GlobalData.Program.BrainstormHomeDir]);
            end
        end
        argout1 = defaultsDir;
        
    case 'UserReportsDir'
        reportDir = bst_fullfile(bst_get('BrainstormUserDir'), 'reports');
        if ~isdir(reportDir)
            res = mkdir(reportDir);
            if ~res
                error(['Cannot create user reports directory: "' reportDir '".']); 
            end
        end
        argout1 = reportDir;
        
    case 'UserMexDir'
        mexDir = bst_fullfile(bst_get('BrainstormUserDir'), 'mex');
        if ~isdir(mexDir)
            res = mkdir(mexDir);
            if ~res
                error(['Cannot create Brainstorm mex-files directory: "' mexDir '".']); 
            end
        end
        argout1 = mexDir;
        
    case 'UserProcessDir'
        processDir = bst_fullfile(bst_get('BrainstormUserDir'), 'process');
        if ~isdir(processDir)
            res = mkdir(processDir);
            if ~res
                error(['Cannot create Brainstorm custom processes directory: "' processDir '".']); 
            end
        end
        argout1 = processDir;
        
    case 'UserDefaultsDir'
        defDir = bst_fullfile(bst_get('BrainstormUserDir'), 'defaults');
        defDirAnat = bst_fullfile(defDir, 'anatomy');
        defDirEeg  = bst_fullfile(defDir, 'eeg');
        if ~isdir(defDir)
            res = mkdir(defDir);
            if ~res
                error(['Cannot create user templates directory: "' defDir '".']); 
            end
        end
        if ~isdir(defDirAnat)
            res = mkdir(defDirAnat);
            if ~res
                error(['Cannot create user templates directory: "' defDirAnat '".']); 
            end
        end
        if ~isdir(defDirEeg)
            res = mkdir(defDirEeg);
            if ~res
                error(['Cannot create user templates directory: "' defDirEeg '".']); 
            end
        end
        argout1 = defDir;
        
    case 'UserPluginsDir'
        pluginsDir = bst_fullfile(bst_get('BrainstormUserDir'), 'plugins');
        if ~isdir(pluginsDir)
            res = mkdir(pluginsDir);
            if ~res
                error(['Cannot create plugins directory: "' pluginsDir '".']); 
            end
        end
        argout1 = pluginsDir;
        
    case 'BrainstormDbFile'
        argout1 = bst_fullfile(bst_get('BrainstormUserDir'), 'brainstorm.mat');

%% ==== PROTOCOL ====
    case 'iProtocol'
        if isempty(GlobalData.DataBase.iProtocol)
            argout1 = 0;
        else
            argout1 = GlobalData.DataBase.iProtocol;
        end
        
    case 'Protocol'
        if ~isempty(GlobalData.DataBase.ProtocolInfo)
            argout1 = find(strcmpi({GlobalData.DataBase.ProtocolInfo.Comment}, varargin{2}));
        else
            argout1 = [];
        end
        
    case {'ProtocolInfo', 'ProtocolSubjects', 'ProtocolStudies', 'isProtocolLoaded', 'isProtocolModified'}
        argout2 = GlobalData.DataBase.iProtocol;
        % No protocol: return empty matrix
        if isempty(argout2) || ~isnumeric(argout2) || argout2 == 0
            return;
        end
        % Check index integrity
        if ((argout2 <= 0) || (argout2 > length(GlobalData.DataBase.ProtocolInfo))), warning('Brainstorm:InvalidIndex', 'Invalid index'), return, end
        % Get requested protocol structure
        argout1 = GlobalData.DataBase.(contextName)(argout2);

        
%% ==== STUDY ====
    % Usage: [sStudy, iStudy] = bst_get('Study', StudyFileName)
    %        [sStudy, iStudy] = bst_get('Study')
    %        [sStudy, iStudy] = bst_get('Study', iStudies)
    case 'Study'
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Get list of current protocols
        ProtocolInfo    = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        ProtocolStudies = GlobalData.DataBase.ProtocolStudies(GlobalData.DataBase.iProtocol);
        % Get list of current protocol studies
        if isempty(ProtocolStudies) || isempty(ProtocolInfo)
            return;
        end
        % ===== PARSE INPUTS =====
        if (nargin < 2)
            % Call: bst_get('Study');
            iStudies = ProtocolInfo.iStudy;
            StudyFileName = [];
        elseif (isnumeric(varargin{2})) 
            iStudies = varargin{2};
            StudyFileName = [];
        elseif (ischar(varargin{2}))
            iStudies = [];
            StudyFileName = strrep(varargin{2}, ProtocolInfo.STUDIES, '');
        end
        % Indices
        iAnalysisStudy = -2;    % CANNOT USE -1 => DISABLES SEARCH FUNCTIONS
        iDefaultStudy  = -3;
        % Indices > 0: normal studies indiced in ProtocolStudies.Study array
            
        % ===== GET STUDY BY INDEX =====
        % Call: bst_get('Study', iStudies);
        if ~isempty(iStudies)
            argout1 = repmat(ProtocolStudies.DefaultStudy, 0);
            % Get analysis study
            iTargetAnalysis = find(iStudies == iAnalysisStudy);
            if ~isempty(iTargetAnalysis)
                argout1(iTargetAnalysis) = repmat(ProtocolStudies.AnalysisStudy, size(iTargetAnalysis));
                argout2(iTargetAnalysis) = repmat(iAnalysisStudy, size(iTargetAnalysis));
            end
            % Get default study
            iTargetDefault = find(iStudies == iDefaultStudy);
            if ~isempty(iTargetDefault) 
                argout1(iTargetDefault) = repmat(ProtocolStudies.DefaultStudy, size(iTargetDefault));
                argout2(iTargetDefault) = repmat(iDefaultStudy, size(iTargetDefault));
            end
            % Get normal studies
            iTargetNormal = find((iStudies >= 1) & (iStudies <= length(ProtocolStudies.Study)));
            if ~isempty(iTargetNormal)
                argout1(iTargetNormal) = ProtocolStudies.Study(iStudies(iTargetNormal));
                argout2(iTargetNormal) = iStudies(iTargetNormal);
            end
            % Error
            if isempty(argout1)
                GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol).iStudy = [];
            end
            
        % ===== GET STUDY BY FILENAME =====
        % Call: bst_get('Study', StudyFileName);
        elseif ~isempty(StudyFileName)
            % NORMAL STUDY
            iStudy = find(file_compare({ProtocolStudies.Study.FileName}, StudyFileName), 1);
            % If a study is found : return it
            if ~isempty(iStudy)
                argout1 = ProtocolStudies.Study(iStudy);
                argout2   = iStudy;
            % DEFAULT STUDY
            elseif ~isempty(ProtocolStudies.DefaultStudy) && file_compare({ProtocolStudies.DefaultStudy.FileName}, StudyFileName)
                argout1 = ProtocolStudies.DefaultStudy;
                argout2   = iDefaultStudy;
            % ANALYSIS STUDY
            elseif ~isempty(ProtocolStudies.AnalysisStudy) && file_compare({ProtocolStudies.AnalysisStudy.FileName}, StudyFileName)
                argout1 = ProtocolStudies.AnalysisStudy;
                argout2   = iAnalysisStudy;
            end
        else
            return
        end
 
        
%% ==== STUDY WITH SUBJECT FILE ====
    % Usage : [sStudies, iStudies] = bst_get('StudyWithSubject', SubjectFile) : WITHOUT the system studies ('intra_subject', 'default_study')
    %         [sStudies, iStudies] = bst_get(..., 'intra_subject', 'default_study') : WITH the system studies: 'intra_subject' | 'default_study'
    case 'StudyWithSubject'
        % Parse inputs
        if (nargin < 2) || ~ischar(varargin{2})
            error('Invalid call to bst_get()');
        end
        if (nargin > 2)
            IntraStudies   = any(strcmpi(varargin(3:end), 'intra_subject'));
            DefaultStudies = any(strcmpi(varargin(3:end), 'default_study'));
        else
            IntraStudies   = 0;
            DefaultStudies = 0;
        end
        SubjectFile = {varargin{2}};
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Get list of current protocol description
        ProtocolInfo    = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        ProtocolStudies = GlobalData.DataBase.ProtocolStudies(GlobalData.DataBase.iProtocol);
        if isempty(ProtocolStudies) || isempty(ProtocolInfo)
            return;
        end
        
        % Get default subject
        sDefaultSubject = bst_get('Subject', 0);
        % If SubjectFile is the default subject filename
        if ~isempty(sDefaultSubject) && ~isempty(sDefaultSubject.FileName) && file_compare( SubjectFile{1}, sDefaultSubject.FileName)
            % Get all the subjects files that use default anatomy
            ProtocolSubjects = GlobalData.DataBase.ProtocolSubjects(GlobalData.DataBase.iProtocol);
            iSubjectUseDefaultAnat = find([ProtocolSubjects.Subject.UseDefaultAnat]);
            if isempty(iSubjectUseDefaultAnat)
                return
            end
            SubjectFile = {ProtocolSubjects.Subject(iSubjectUseDefaultAnat).FileName};
            % Also updates inter-subject node
            isInterSubject = 1;
        else
            isInterSubject = 0;
        end
        % Search all the current protocol's studies
        iStudies = [];
        for i=1:length(SubjectFile)
            iStudies = [iStudies, find(file_compare({ProtocolStudies.Study.BrainStormSubject}, SubjectFile{i}))];
        end
        % Return results
        if ~isempty(iStudies)
            % Remove "analysis_intra" and "default_study" studies from list
            if ~IntraStudies
                iStudies(strcmpi({ProtocolStudies.Study(iStudies).Name}, bst_get('DirAnalysisIntra'))) = [];
            end
            if ~DefaultStudies
                iStudies(strcmpi({ProtocolStudies.Study(iStudies).Name}, bst_get('DirDefaultStudy'))) = [];
            end
            % Return studies
            argout1 = ProtocolStudies.Study(iStudies);
            argout2   = iStudies;
        else
            argout1 = repmat(db_template('Study'), 0);
            argout2   = [];
        end
        % Add inter-subject node, if needed
        if isInterSubject
            [sInterStudy, iInterStudy] = bst_get('AnalysisInterStudy');
            argout1 = [argout1, sInterStudy];
            argout2   = [argout2,   iInterStudy];
        end
              
        
%% ==== STUDY WITH CONDITION PATH ====
    % USAGE:  [sStudies, iStudies] = bst_get('StudyWithCondition', ConditionPath)
    %
    % INPUT: ConditionPath
    %    - 'SubjectName/conditionName'  : Target condition for the specified subject
    %    - 'SubjectName/@intra'         : Intra-subject condition for the subject
    %    - 'SubjectName/@default_study' : Default condition for the subject (where the subject's shared files are stored)
    %    - '*/conditionName'            : Target condition for all the subjects
    %    - '@inter'                     : Inter-subject condition
    %    - '@default_study'             : Protocol's default condition (where the protocol's shared files are stored)
    
    case 'StudyWithCondition'
        % Parse inputs
        if (nargin ~= 2) || ~ischar(varargin{2})
            error('Invalid call to bst_get()');
        end
        ConditionPath = varargin{2};
        % Get list of current protocol description
        ProtocolInfo    = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        ProtocolStudies = GlobalData.DataBase.ProtocolStudies(GlobalData.DataBase.iProtocol);
        if isempty(ProtocolStudies) || isempty(ProtocolInfo)
            return;
        end

        % ConditionPath = @inter
        if strcmpi(ConditionPath, '@inter')
            iStudy     = -2;
            argout2   = iStudy;
            argout1 = bst_get('Study', iStudy);
        % ConditionPath = @default_study
        elseif strcmpi(ConditionPath, '@default_study')
            iStudy     = -3;
            argout2   = iStudy;
            argout1 = bst_get('Study', iStudy);
        % ConditionPath = SubjectName/ConditionName
        else 
            % Get subject and condition names
            condSplit = str_split(ConditionPath);
            if (length(condSplit) ~= 2)
                error('Invalid condition path.');
            end
            SubjectName = condSplit{1};
            ConditionName = condSplit{2};

            % If first element is '*', search for condition in all the studies
            if (SubjectName(1) == '*')
                iStudies = 1:length(ProtocolStudies.Study);
            % Else : search for condition only in studies that are linked to the subject specified in the ConditionPath
            else
                % Get subject
                sSubject = bst_get('Subject', SubjectName, 1);
                if isempty(sSubject)
                    return;
                end
                iStudies = find(file_compare({ProtocolStudies.Study.BrainStormSubject}, sSubject.FileName));
            end
            % Nothing to search
            if isempty(iStudies)
                return
            end

            % Search all the current protocol's studies
            iStudies = iStudies(cellfun(@(c)isequal(ConditionName, c), [ProtocolStudies.Study(iStudies).Condition]));
            % Return results
            if ~isempty(iStudies)
                % Remove "analysis_intra" and "default_study" studies from list
                if ~strcmpi(ConditionName, '@intra')
                    iStudies(strcmpi({ProtocolStudies.Study(iStudies).Condition}, bst_get('DirAnalysisIntra'))) = [];
                end
                if ~strcmpi(ConditionName, '@default_study')
                    iStudies(strcmpi({ProtocolStudies.Study(iStudies).Condition}, bst_get('DirDefaultStudy'))) = [];
                end
                % Sort by subject
                if (length(iStudies) > 1)
                    SubjNameList = cell(1,length(iStudies));
                    % For each study, get subject name
                    for i = 1:length(iStudies)
                        sSubject = bst_get('Subject', ProtocolStudies.Study(iStudies(i)).BrainStormSubject);
                        SubjNameList{i} = sSubject.Name;
                    end
                    % Sort subjects names
                    [sortSubjList, iSort] = sort(SubjNameList);
                    % Apply same sorting to studies
                    iStudies = iStudies(iSort);
                end
                % Return studies
                argout1 = ProtocolStudies.Study(iStudies);
                argout2   = iStudies;
            else
                argout1 = repmat(db_template('Study'), 0);
                argout2   = [];
            end
        end

%% ==== CHANNEL STUDIES WITH SUBJECT ====
    % Usage: iStudies = bst_get('ChannelStudiesWithSubject', iSubjects, 'NoIntra')
    case 'ChannelStudiesWithSubject'
        % Parse inputs
        if (nargin >= 2) && isnumeric(varargin{2})
            iSubjects = varargin{2};
        else
            error('Invalid call to bst_get()');
        end
        if (nargin == 3) && strcmpi(varargin{3}, 'NoIntra')
            NoIntra = 1;
        else
            NoIntra = 0;
        end
        % Process all subjects
        iStudies = [];
        for i=1:length(iSubjects)
            iSubject = iSubjects(i);
            sSubject = bst_get('Subject', iSubject, 1);
            % No subject: error
            if isempty(sSubject) 
                continue
            % If subject uses default channel file    
            elseif (sSubject.UseDefaultChannel ~= 0)
                % Get default study for this subject
                [tmp___, iStudiesNew] = bst_get('DefaultStudy', iSubject);
                iStudies = [iStudies, iStudiesNew];
            % Else: get all the studies belonging to this subject
            else
                if NoIntra
                    [tmp___, iStudiesNew] = bst_get('StudyWithSubject', sSubject.FileName);
                else
                    [tmp___, iStudiesNew] = bst_get('StudyWithSubject', sSubject.FileName, 'intra_subject');
                end
                iStudies = [iStudies, iStudiesNew];
            end
        end
        argout1 = iStudies;
    
        
%% ==== STUDIES COUNT ====
    % Usage: [nbStudies] = bst_get('StudyCount')
    case 'StudyCount'
        % Nothing
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            argout1 = 0;
            return;
        end
        % Get list of current protocol studies
        ProtocolStudies = GlobalData.DataBase.ProtocolStudies(GlobalData.DataBase.iProtocol);
        argout1 = length(ProtocolStudies.Study);

%% ==== SUBJECTS COUNT ====
    % Usage: [nbSubjects] = bst_get('SubjectCount')
    case 'SubjectCount'
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            argout1 = 0;
            return;
        end
        % Get list of current protocol studies
        ProtocolSubjects = GlobalData.DataBase.ProtocolSubjects(GlobalData.DataBase.iProtocol);
        argout1 = length(ProtocolSubjects.Subject);
        
%% ==== NORMALIZED SUBJECT ====
    case 'NormalizedSubject'
        % Get normalized subject name
        normSubjName = 'Group_analysis';
        % Try to get normalized subject
        [sNormSubj, iNormSubj] = bst_get('Subject', normSubjName, 0);
        % If normalized subject does not exist: create it
        if isempty(sNormSubj)
            % Always use default anatomy
            UseDefaultAnat = 1;
            % If all the subjects use a global channel file: Use global default as well
            if ~isempty(GlobalData.DataBase.ProtocolSubjects(GlobalData.DataBase.iProtocol).Subject) && ...
                all([GlobalData.DataBase.ProtocolSubjects(GlobalData.DataBase.iProtocol).Subject.UseDefaultChannel] == 2)
                UseDefaultChannel = 2;
            else
                UseDefaultChannel = 1;
            end    
            % Create subject
            [sNormSubj, iNormSubj] = db_add_subject(normSubjName, [], UseDefaultAnat, UseDefaultChannel);
            % Get full subject structure
            [sNormSubj, iNormSubj] = bst_get('Subject', normSubjName, 0);
        end
        argout1 = sNormSubj;
        argout2 = iNormSubj;
        
        
%% ==== ANALYSIS STUDY (INTRA) ====
    % Usage: [sAnalStudy, iAnalStudy] = bst_get('AnalysisIntraStudy', iSubject) 
    case 'AnalysisIntraStudy'
        % Parse inputs
        if (nargin == 2) && isnumeric(varargin{2})
            iSubject = varargin{2};
        else
            error('Invalid call to bst_get()');
        end
        % Get subject
        sSubject = bst_get('Subject', iSubject, 1);
        % Get studies related to subject
        [sSubjStudies, iSubjStudies] = bst_get('StudyWithSubject', sSubject.FileName, 'intra_subject');
        % Look for the 'AnalysisIntra' study
        iFound = find(cellfun(@(c)ismember(bst_get('DirAnalysisIntra'), c), {sSubjStudies.Condition}));
        iAnalStudy = iSubjStudies(iFound);
        sAnalStudy = sSubjStudies(iFound);
        % Return found structure
        argout1 = sAnalStudy;
        argout2 = iAnalStudy;        
        
        
%% ==== ANALYSIS STUDY (INTER) ====
    % Usage: [sAnalStudyInter, iAnalStudyInter] = bst_get('AnalysisInterStudy') 
    case 'AnalysisInterStudy'
        iAnalStudyInter = -2;
        [argout1, argout2] = bst_get('Study', iAnalStudyInter);
        
       
%% ==== DEFAULT STUDY ====
    % Usage: [sDefaulStudy, iDefaultStudy] = bst_get('DefaultStudy', iSubject)
    %        [sDefaulStudy, iDefaultStudy] = bst_get('DefaultStudy')           : iSubject=0
    %        [sDefaulStudy, iDefaultStudy] = bst_get('DefaultStudy', SubjectFile)
    case 'DefaultStudy'
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Parse inputs
        if (nargin == 1)
            iSubject = 0;
        elseif (nargin == 2) && isnumeric(varargin{2})
            iSubject = varargin{2};
        elseif (nargin == 2) && ischar(varargin{2})
            SubjectFile = varargin{2};
            % Get subject attached to study
            [sSubject, iSubject] = bst_get('Subject', SubjectFile, 1);
            if isempty(sSubject) || ~sSubject.UseDefaultChannel
                return;
            end
        else
            error('Invalid call to bst_get()');
        end
        % === DEFAULT SUBJECT ===
        % => Return global default study
        if (iSubject == 0)
            % Get protocol's studies
            ProtocolStudies = GlobalData.DataBase.ProtocolStudies(GlobalData.DataBase.iProtocol);
            % Return Global default study
            argout1 = ProtocolStudies.DefaultStudy;
            argout2   = -3;
        % === NORMAL SUBJECT ===
        else
            % Get subject
            sSubject = bst_get('Subject', iSubject, 1);
            % === GLOBAL DEFAULT STUDY ===
            if sSubject.UseDefaultChannel == 2
                % Get protocol's studies
                ProtocolStudies = GlobalData.DataBase.ProtocolStudies(GlobalData.DataBase.iProtocol);
                % Return Global default study
                argout1 = ProtocolStudies.DefaultStudy;
                argout2   = -3;
            % === SUBJECT'S DEFAULT STUDY ===
            elseif sSubject.UseDefaultChannel == 1
                % Get studies related to subject
                [sSubjStudies, iSubjStudies] = bst_get('StudyWithSubject', sSubject.FileName, 'default_study');
                % Look for the 'DefaultStudy' study
                iFound = find(cellfun(@(c)ismember(bst_get('DirDefaultStudy'), c), {sSubjStudies.Condition}));
                iDefaultStudy = iSubjStudies(iFound);
                sDefaultStudy = sSubjStudies(iFound);
                % Return found structure
                argout1 = sDefaultStudy;
                argout2   = iDefaultStudy;        
            end
        end
        
        
        
%% ==== SUBJECT ====
    % Usage : [sSubject, iSubject] = bst_get('Subject', iSubject,        isRaw)
    %         [sSubject, iSubject] = bst_get('Subject', SubjectFileName, isRaw);
    %         [sSubject, iSubject] = bst_get('Subject', SubjectName,     isRaw);
    %         [sSubject, iSubject] = bst_get('Subject');
    % If isRaw is set: force to return the real brainstormsubject description
    % (ignoring wether it uses protocol's default anatomy or not)
    case 'Subject' 
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
         % Get list of current protocol subjects
        ProtocolSubjects = GlobalData.DataBase.ProtocolSubjects(GlobalData.DataBase.iProtocol);
        sSubject = [];
        SubjectName = [];
        SubjectFileName = [];
        % ISRAW parameter
        if (nargin < 3)
            isRaw = 0;
        else
            isRaw = varargin{3};
        end
        % Call: bst_get('subject', iSubject, isRaw);
        if (nargin >= 2) && isnumeric(varargin{2})
            iSubject = varargin{2};
            if (iSubject > length(ProtocolSubjects.Subject))
                error('Invalid subject indice.');
            end
            % If required subject is default subject (iSubject = 0)
            if (iSubject == 0)
                % Default subject available
                if ~isempty(ProtocolSubjects.DefaultSubject)
                    sSubject = ProtocolSubjects.DefaultSubject;
                % Default subject not available
                else
                    return
                end
            % Normal subject 
            else
                sSubject = ProtocolSubjects.Subject(iSubject);
            end
            
        % Call: bst_get('subject', SubjectFileName, isRaw);
        % Call: bst_get('subject', SubjectName,     isRaw);
        elseif (nargin >= 2) && isempty(varargin{2})
            % If study name is empty: use DefaultSubject
            SubjectFileName = ProtocolSubjects.DefaultSubject.FileName;
        elseif (nargin >= 2) && (ischar(varargin{2}))
            [fName, fBase, fExt] = bst_fileparts(varargin{2});
            % Argument is a Matlab .mat filename
            if strcmpi(fExt, '.mat')
                SubjectFileName = varargin{2};
            % Else : assume argument is a directory
            else
                SubjectName = file_standardize(varargin{2});
            end
                            
        % Call: bst_get('subject');   => looking for current subject 
        elseif (nargin < 2)
            % Get current subject filename in current study
            sStudy = bst_get('Study');
            if isempty(sStudy)
                return
            end
            SubjectFileName = sStudy.BrainStormSubject;
            % If study's subject is not defined, get DefaultSubject
            if isempty(SubjectFileName) && ~isempty(ProtocolSubjects.DefaultSubject)
                SubjectFileName = ProtocolSubjects.DefaultSubject.FileName;
            end
        else
            error('Invalid call to bst_get()');
        end

        % If Subject is defined by its filename/name
        if isempty(sSubject)
            % Look in Default Subject
            if ~isempty(ProtocolSubjects.DefaultSubject) && (file_compare(ProtocolSubjects.DefaultSubject.FileName, SubjectFileName) ...
                                                          || strcmpi(ProtocolSubjects.DefaultSubject.Name, SubjectName))
                sSubject = ProtocolSubjects.DefaultSubject;
                iSubject = 0;
            % If not found : find target subject file name in normal subjects
            elseif ~isempty(SubjectFileName)
                iSubject = find(file_compare({ProtocolSubjects.Subject.FileName}, SubjectFileName), 1);
                sSubject = ProtocolSubjects.Subject(iSubject);
            elseif ~isempty(SubjectName)
                iSubject = find(file_compare({ProtocolSubjects.Subject.Name}, SubjectName), 1);
                sSubject = ProtocolSubjects.Subject(iSubject);
            else
                error('Subject name not specified.');
            end
        end
        
        % Return found subject
        if ~isempty(iSubject) && ~isempty(sSubject)
            % If subject uses default subject
            if sSubject.UseDefaultAnat && ~isRaw && ~isempty(ProtocolSubjects.DefaultSubject) && ~isempty(ProtocolSubjects.DefaultSubject.FileName)
                % Return default subject (WITH REAL SUBJECT'S NAME)
                argout1                   = ProtocolSubjects.DefaultSubject;
                argout1.Name              = sSubject.Name;
                argout1.UseDefaultAnat    = sSubject.UseDefaultAnat;
                argout1.UseDefaultChannel = sSubject.UseDefaultChannel;
                argout2                     = iSubject;
            % Else, return found subject
            else
                argout1  = sSubject;
                argout2    = iSubject;
            end
        end

        
%% ==== SURFACE FILE ====
    % Usage : [sSubject, iSubject, iSurface] = bst_get('SurfaceFile', SurfaceFile)
    case 'SurfaceFile'
        % No protocol in database
        if isempty(GlobalData) || isempty(GlobalData.DataBase) || isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Get list of current protocol subjects
        ProtocolSubjects = GlobalData.DataBase.ProtocolSubjects(GlobalData.DataBase.iProtocol);
        if isempty(ProtocolSubjects)
            return
        end;
        
        % Parse inputs
        if (nargin == 2)
            SurfaceFile = varargin{2};
        else
            error('Invalid call to bst_get().');
        end

        % Remove SUBJECTS path from SurfaceFile
        SurfaceFile = file_short(SurfaceFile);
        % Look for surface file in DefaultSubject
        if ~isempty(ProtocolSubjects.DefaultSubject)
            % Find the first surface that matches the SurfaceFile
            iSurface = find(file_compare(SurfaceFile, {ProtocolSubjects.DefaultSubject.Surface.FileName}), 1);
            % If a surface was found in default subject : return it
            if ~isempty(iSurface)
                argout1  = ProtocolSubjects.DefaultSubject;
                argout2    = 0;
                argout3 = iSurface;
                return
            end
        end
        % Look for surface file in all the surfaces of all subjects
        for iSubj = 1:length(ProtocolSubjects.Subject)
            % Find the first surface that matches the SurfaceFile
            iSurface = find(file_compare(SurfaceFile, {ProtocolSubjects.Subject(iSubj).Surface.FileName}), 1);
            % If a surface was found in current subject : return it
            if ~isempty(iSurface)
                argout1  = ProtocolSubjects.Subject(iSubj);
                argout2    = iSubj;
                argout3 = iSurface;
                return
            end
        end
            
        
%% ==== SURFACE FILE BY TYPE ====
    % Usage : [sSurface, iSurface] = bst_get('SurfaceFileByType', iSubject,    SurfaceType)
    %         [sSurface, iSurface] = bst_get('SurfaceFileByType', SubjectFile, SurfaceType)
    %         [sSurface, iSurface] = bst_get('SurfaceFileByType', SurfaceFile, SurfaceType)
    %         [sSurface, iSurface] = bst_get('SurfaceFileByType', MriFile,     SurfaceType)
    %         [sSurface, iSurface] = bst_get('SurfaceFileByType', ...,         SurfaceType, isDefaultOnly)
    case 'SurfaceFileByType'
        % By default: return only the default surfaces of the category
        if (nargin < 4)
            isDefaultOnly = 1;
        else
            isDefaultOnly = varargin{4};
        end
        % Get subject
        if isempty(varargin{2})
            % Get default subject
            sSubject = bst_get('Subject', 0);
        elseif ischar(varargin{2})
            FileName = varargin{2};
            sSubject = bst_get('AnyFile', FileName);
        else
            iSubject = varargin{2};
            sSubject = bst_get('Subject', iSubject);
        end
        % Error handling
        if isempty(sSubject)
            disp('BST> Warning: Subject not found.');
            return;
        elseif isempty(sSubject.Surface)
            return;
        end
        SurfaceType = varargin{3};
        
        % === RETURN ONLY DEFAULTS ===
        if isDefaultOnly
            % Look for required surface type
            field = ['i' SurfaceType];
            if ~isfield(sSubject, field) || isempty(sSubject.(field))
                return
            end
            argout1 = sSubject.Surface(sSubject.(field));
            argout2 = sSubject.(field); 
        % === RETURN ALL THE SURFACES ===
        else
            % Build the list of tagged surfaces
            fileTag = ['_' lower(SurfaceType)];
            iTargetList = find(cellfun(@(c)~isempty(strfind(c, fileTag)), {sSubject.Surface.FileName}));
            % Put the default cortex on top of the list
            iDefaults = intersect([sSubject.iCortex, sSubject.iScalp, sSubject.iInnerSkull, sSubject.iOuterSkull, sSubject.iFibers, sSubject.iFEM], iTargetList);
            if ~isempty(iDefaults)
                iTargetList = [iDefaults, setdiff(iTargetList, iDefaults)];
            end
            % Return all cortex surfaces
            argout1 = sSubject.Surface(iTargetList);
            argout2 = iTargetList; 
        end
        
        
%% ==== MRI FILE ====
    % Usage : [sSubject, iSubject, iMri] = bst_get('MriFile', MriFile)
    case 'MriFile'
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Get list of current protocol subjects
        ProtocolSubjects = GlobalData.DataBase.ProtocolSubjects(GlobalData.DataBase.iProtocol);
        if isempty(ProtocolSubjects)
            return
        end
        
        % Parse inputs
        if (nargin == 2)
            MriFile = varargin{2};
        else
            error('Invalid call to bst_get().');
        end

        % Remove SUBJECTS path from MriFile
        MriFile = file_short(MriFile);
        % Look for MRI file in DefaultSubject
        if ~isempty(ProtocolSubjects.DefaultSubject)
            % Find the first MRI that matches the MriFile
            iMri = find(file_compare(MriFile, {ProtocolSubjects.DefaultSubject.Anatomy.FileName}), 1);
            % If a MRI was found in default subject : return it
            if ~isempty(iMri)
                argout1  = ProtocolSubjects.DefaultSubject;
                argout2    = 0;
                argout3 = iMri;
                return
            end
        end
        % Look for MRI file in all the MRIs of all subjects
        for iSubj = 1:length(ProtocolSubjects.Subject)
            % Find the first MRI that matches the MriFile
            iMri = find(file_compare(MriFile, {ProtocolSubjects.Subject(iSubj).Anatomy.FileName}), 1);
            % If a MRI was found in current subject : return it
            if ~isempty(iMri)
                argout1  = ProtocolSubjects.Subject(iSubj);
                argout2    = iSubj;
                argout3 = iMri;
                return
            end
        end
        
        
%% ==== CHANNEL FILE ====
    % Usage: [sStudy, iStudy, iChannel] = bst_get('ChannelFile', ChannelFile)
    case 'ChannelFile'
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        % Parse inputs
        if (nargin == 2)
            ChannelFile = varargin{2};
            ChannelFile = strrep(ChannelFile, ProtocolInfo.STUDIES, '');
        else
            error('Invalid call to bst_get().');
        end
        % Look for Channel file in all the surfaces of all subjects
        [argout1, argout2, argout3] = findFileInStudies('Channel', 'FileName', ChannelFile);
        
        
%% ==== CHANNEL FILE FOR STUDY ====
    % Usage: [ChannelFile, sStudy, iStudy] = bst_get('ChannelFileForStudy', StudyFile/DataFile)
    case 'ChannelFileForStudy'
        % Parse inputs
        if (nargin == 2)
            StudyFile = varargin{2};
        else
            error('Invalid call to bst_get().');
        end
        % Get study in database
        [sStudy, iStudy] = bst_get('Study', StudyFile);
        % If data file instead on Study file
        if isempty(sStudy)
            [sStudy, iStudy] = bst_get('AnyFile', StudyFile);
        end
        sChannel = bst_get('ChannelForStudy', iStudy);
        if ~isempty(sChannel)
            argout1 = sChannel.FileName;
            argout2 = sStudy;
            argout3 = iStudy;
        else
            argout1 = [];
        end
        
        
%% ==== CHANNEL STRUCT FOR STUDY ====
    % Usage: [sChannel, iChanStudy] = bst_get('ChannelForStudy', iStudies)
    case 'ChannelForStudy'
        % Parse inputs
        if (nargin == 2)
            iStudies = varargin{2};
        else
            error('Invalid call to bst_get().');
        end
        iChanStudies = [];
        sListChannel = [];
        for i = 1:length(iStudies)           
            % Get study 
            iStudy = iStudies(i);
            sStudy = bst_get('Study', iStudy);
            if isempty(sStudy)
                continue;
            end
            iChanStudy = iStudy;
            % === Analysis-Inter node ===
            iAnalysisInter      = -2;
            iGlobalDefaultStudy = -3;
            if (iStudy == iAnalysisInter)
                % If no channel file is defined in 'Analysis-intra' node: look in 
                if isempty(sStudy.Channel)
                    % Get global default study
                    sStudy = bst_get('Study', iGlobalDefaultStudy);
                    iChanStudy = iGlobalDefaultStudy;
                end
            % === All other nodes ===
            else
                % Get subject attached to study
                [sSubject, iSubject] = bst_get('Subject', sStudy.BrainStormSubject, 1);
                if isempty(sSubject)
                    return;
                end
                % Subject uses default channel/headmodel
                if (sSubject.UseDefaultChannel ~= 0)
                    [sStudy, iChanStudy] = bst_get('DefaultStudy', iSubject);
                    if isempty(sStudy)
                        return
                    end
                end
            end
            iChanStudies = [iChanStudies, iChanStudy];
            sListChannel = [sListChannel, sStudy.Channel];
        end
        % Return Channel structure
        argout1 = sListChannel;
        argout2 = iChanStudies;

%% ==== CHANNEL MODALITIES =====
    % Usage: [Modalities, DispMod, DefMod] = bst_get('ChannelModalities', ChannelFile)
    %        [Modalities, DispMod, DefMod] = bst_get('ChannelModalities', DataFile/ResultsFile/TimefreqFile...)
    case 'ChannelModalities'
        % Get input file
        [sStudy, iStudy, iItem, DataType, sItem] = bst_get('AnyFile', varargin{2});
        % If channel file
        if strcmpi(DataType, 'channel')
            sChannel = sItem;
        else
            sChannel = bst_get('ChannelForStudy', iStudy);
        end
        % Return modalities
        if ~isempty(sChannel)
            % Get all modalities
            if ~isempty(sChannel.DisplayableSensorTypes)
                % Return the displayable sensors on top of the list
                argout1 = cat(2, sChannel.DisplayableSensorTypes, setdiff(sChannel.Modalities, sChannel.DisplayableSensorTypes));
            else
                argout1 = sChannel.Modalities;
            end
            % Get only sensors that have spatial representation
            argout2 = sChannel.DisplayableSensorTypes;
            % Default candidates
            if ~isempty(argout2)
                defList = argout2;
            else
                defList = argout1;
            end
            if isempty(defList)
                return;
            end
            % Remove EDF and BDF from the default list
            defList = setdiff(defList, {'EDF','BDF','KDF'});
            % Get default modality
            if ismember('SEEG', defList)
                argout3 = 'SEEG';
            elseif ismember('ECOG', defList)
                argout3 = 'ECOG';
            elseif any(ismember({'MEG','MEG GRAD','MEG MAG'}, defList))
                argout3 = 'MEG';
            elseif ismember('EEG', defList)
                argout3 = 'EEG';
            elseif ismember('NIRS', defList)
                argout3 = 'NIRS';
            else
                argout3 = defList{1};
            end
            % Place the default on top of the lists
            if ismember(argout3, argout1)
                argout1(strcmpi(argout1, argout3)) = [];
                argout1 = cat(2, argout3, argout1);
            end
            if ismember(argout3, argout2)
                argout2(strcmpi(argout2, argout3)) = [];
                argout2 = cat(2, argout3, argout2);
            end
        else
            argout1 = [];
        end
        

%% ==== TIMEFREQ DISPLAY MODALITIES ====
    % Usage: DisplayMod = bst_get('TimefreqDisplayModalities', TimefreqFile)
    case 'TimefreqDisplayModalities'
        TimefreqFile = varargin{2};
        % Load sensor names from file
        TimefreqMat = in_bst_timefreq(TimefreqFile, 0, 'RowNames');
        % Get channel file
        ChannelFile = bst_get('ChannelFileForStudy', TimefreqFile);
        if isempty(ChannelFile)
            return;
        end
        % Load channel file
        ChannelMat = load(file_fullpath(ChannelFile), 'Channel');
        % Get channels that are present in the file
        [tmp__,I,J] = intersect({ChannelMat.Channel.Name}, TimefreqMat.RowNames);
        FileMod = unique({ChannelMat.Channel(I).Type});
        % Check if only one type of gradiometer is selected
        if isequal(FileMod, {'MEG GRAD'}) && all(cellfun(@(c)(c(end)=='2'), {ChannelMat.Channel(I).Name}))
            argout1 = {'MEG GRAD2'};
        elseif isequal(FileMod, {'MEG GRAD'}) && all(cellfun(@(c)(c(end)=='3'), {ChannelMat.Channel(I).Name}))
            argout1 = {'MEG GRAD3'};
        % Keep only the modalities that can be displayed (as topography)
        else
            argout1 = intersect(FileMod, {'MEG','MEG GRAD','MEG MAG','EEG','ECOG','SEEG','NIRS'});
        end
        
        
%% ==== CHANNEL DEVICE ====
    % Usage: Device = bst_get('ChannelDevice', ChannelFile)
    case 'ChannelDevice'
        ChannelFile = varargin{2};
        if ~isempty(strfind(ChannelFile, 'vectorview306'))
            Device = 'Vectorview306';
        elseif ~isempty(strfind(ChannelFile, 'ctf_acc1'))
            Device = 'CTF';
        elseif ~isempty(strfind(ChannelFile, '4d_acc1'))
            Device = '4D';
        elseif ~isempty(strfind(ChannelFile, 'babysquid'))
            Device = 'BabySQUID';
        elseif ~isempty(strfind(ChannelFile, 'babymeg'))
            Device = 'BabyMEG';
        elseif ~isempty(strfind(ChannelFile, 'kit'))
            Device = 'KIT';
        elseif ~isempty(strfind(ChannelFile, 'ricoh'))
            Device = 'RICOH';
        elseif ~isempty(strfind(ChannelFile, 'kriss'))
            Device = 'KRISS';
        elseif ~isempty(strfind(ChannelFile, 'nirsbrs'))
            Device = 'NIRS-BRS';
        else
            Device = '';
        end
        argout1 = Device;
        

%% ==== HEADMODEL STRUCT FOR STUDY ====
    % Usage: [sHeadModel] = bst_get('HeadModelForStudy', iStudy)
    case 'HeadModelForStudy'
        % Parse inputs
        if (nargin == 2)
            iStudy = varargin{2};
        else
            error('Invalid call to bst_get().');
        end
        % Get study 
        sStudy = bst_get('Study', iStudy);
        % === Analysis-Inter node ===
        iAnalysisInter      = -2;
        iGlobalDefaultStudy = -3;
        if (iStudy == iAnalysisInter)
            % If no channel file is defined in 'Analysis-intra' node: look in 
            if isempty(sStudy.iHeadModel)
                % Get global default study
                sStudy = bst_get('Study', iGlobalDefaultStudy);
            end
        % === All other nodes ===
        else
            % Get subject attached to study
            [sSubject, iSubject] = bst_get('Subject', sStudy.BrainStormSubject, 1);
            if isempty(sSubject)
                return;
            end
            % Subject uses default channel/headmodel
            if (sSubject.UseDefaultChannel ~= 0)
                sStudy = bst_get('DefaultStudy', iSubject);
                if isempty(sStudy)
                    return
                end
            end
        end
        % Return HeadModel structure
        if ~isempty(sStudy.iHeadModel)
            argout1 = sStudy.HeadModel(sStudy.iHeadModel(1));
        else
            argout1 = [];
        end

        
%% ==== HEADMODEL FILE ====
    % Usage: [sStudy, iStudy, iHeadModel] = bst_get('HeadModelFile', HeadModelFile, iStudies)
    %        [sStudy, iStudy, iHeadModel] = bst_get('HeadModelFile', HeadModelFile)
    case 'HeadModelFile'
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Input #2: HeadModelFile
        ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        HeadModelFile = varargin{2};
        HeadModelFile = strrep(HeadModelFile, ProtocolInfo.STUDIES, '');
        % Input #3: iStudies
        if (nargin < 3)
            iStudies = [];
        else
            iStudies = varargin{3};
        end
        % Look for surface file in all the surfaces of all subjects
        [argout1, argout2, argout3] = findFileInStudies('HeadModel', 'FileName', HeadModelFile, iStudies);
  
%% ==== NOISECOV FILE ====
    % Usage: [sStudy, iStudy, iNoiseCov] = bst_get('NoiseCovFile', NoiseCovFile, iStudies)
    %        [sStudy, iStudy, iNoiseCov] = bst_get('NoiseCovFile', NoiseCovFile)
    % Usage: [sStudy, iStudy, iNoiseCov] = bst_get('DataCovFile', NoiseCovFile, iStudies)
    %        [sStudy, iStudy, iNoiseCov] = bst_get('DataCovFile', NoiseCovFile)
    case {'NoiseCovFile', 'DataCovFile'}
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Input #2: NoiseCovFile
        ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        NoiseCovFile = varargin{2};
        NoiseCovFile = strrep(NoiseCovFile, ProtocolInfo.STUDIES, '');
        % Input #3: iStudies
        if (nargin < 3)
            iStudies = [];
        else
            iStudies = varargin{3};
        end
        % Look for surface file in all the surfaces of all subjects
        [argout1, argout2, argout3] = findFileInStudies('NoiseCov', 'FileName', NoiseCovFile, iStudies);

        
%% ==== DATA FILE ====
    % Usage: [sStudy, iStudy, iData] = bst_get('DataFile', DataFile, iStudies)
    %        [sStudy, iStudy, iData] = bst_get('DataFile', DataFile)
    case 'DataFile'
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Input #2: DataFile
        ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        DataFile = varargin{2};
        DataFile = strrep(DataFile, ProtocolInfo.STUDIES, '');
        % Input #3: iStudies
        if (nargin < 3)
            iStudies = [];
        else
            iStudies = varargin{3};
        end
        % Look for file in all the studies
        [argout1, argout2, argout3] = findFileInStudies('Data', 'FileName', DataFile, iStudies);
        

%% ==== DATA FOR DATA LIST ====
    % Usage: [iFoundData] = bst_get('DataForDataList', iStudy, DataListName)
    case 'DataForDataList'
        iStudy = varargin{2};
        DataListName = varargin{3};
        % Get study structure
        sStudy = bst_get('Study', iStudy);
        % Get all the data files held by this datalist
        listComments = cellfun(@(c)deblank(str_remove_parenth(c)), {sStudy.Data.Comment}, 'UniformOutput', 0);
        iFoundData = find(strcmp(listComments, DataListName));
        % Return found data files
        argout1 = iFoundData;

%% ==== MATRIX FOR MATRIX LIST ====
    % Usage: [iFoundMatrix] = bst_get('MatrixForMatrixList', iStudy, MatrixListName)
    case 'MatrixForMatrixList'
        iStudy = varargin{2};
        MatrixListName = varargin{3};
        % Get study structure
        sStudy = bst_get('Study', iStudy);
        % Get all the matrix files held by this datalist
        listComments = cellfun(@(c)deblank(str_remove_parenth(c)), {sStudy.Matrix.Comment}, 'UniformOutput', 0);
        iFoundMatrix = find(strcmp(listComments, MatrixListName));
        % Return found matrix files
        argout1 = iFoundMatrix;
        
        
%% ==== DATA FOR STUDY (INCLUDING SHARED STUDIES) ====
    % Usage: [iStudies, iDatas] = bst_get('DataForStudy', iStudy)
    case 'DataForStudy'
        % Get target study
        iStudy = varargin{2};
        sStudy = bst_get('Study', iStudy);
        isDefaultStudy  = strcmpi(sStudy.Name, bst_get('DirDefaultStudy'));
        isGlobalDefault = (iStudy == -3);
        
        % If study is the global default study
        sStudies = [];
        iStudies = [];
        if isGlobalDefault
            % Get all the subjects of the protocol
            nbSubjects = bst_get('SubjectCount');
            for iSubject = 1:nbSubjects
                sSubject = bst_get('Subject', iSubject, 1);
                if sSubject.UseDefaultChannel
                    [tmp_sStudies, tmp_iStudies] = bst_get('StudyWithSubject', sSubject.FileName);
                    sStudies = [sStudies, tmp_sStudies];
                    iStudies = [iStudies, tmp_iStudies];
                end
            end
        % Else, if study is a subject's default study (ie. channel file is shared by all studies of one subject)
        elseif isDefaultStudy
            % Get all the subject's studies
            [sStudies, iStudies] = bst_get('StudyWithSubject', sStudy.BrainStormSubject, 'intra_subject', 'default_study');
        else
            % Normal: one channel per condition
            sStudies = sStudy;
            iStudies = iStudy;
        end
        % Get all the DataFiles for all these studies
        for i = 1:length(sStudies)
            nData = length(sStudies(i).Data);
            argout1 = [argout1, repmat(iStudies(i), [1,nData])];
            argout2   = [argout2, 1:nData];
        end
       
        
%% ==== DATA FOR STUDIES (INCLUDING SHARED STUDIES) ====
    % Usage: [iStudies, iDatas] = bst_get('DataForStudies', iStudies)
    case 'DataForStudies'
        iStudies = varargin{2};
        for i = 1:length(iStudies)
            [tmp_iStudies, tmp_iDatas] = bst_get('DataForStudy', iStudies(i));
            argout1 = [argout1, tmp_iStudies];
            argout2 = [argout2, tmp_iDatas];
        end
        
%% ==== DATA FILE FOR CHANNEL FILE ====
    % Usage: DataFiles = bst_get('DataForChannelFile', ChannelFile)
    case 'DataForChannelFile'
        ChannelFile = varargin{2};
        DataFiles = {};
        % Get study for the given channel file
        [sStudy, iStudy] = bst_get('ChannelFile', ChannelFile);
        if isempty(sStudy)
            return;
        end
        % Get dependent data files
        [iStudies, iDatas] = bst_get('DataForStudy', iStudy);
        % Get all the Data filenames
        for i = 1:length(iStudies)
            sStudy = bst_get('Study', iStudies(i));
            DataFiles = cat(2, DataFiles, {sStudy.Data(iDatas(i)).FileName});
        end
        argout1 = DataFiles;
                
        
%% ==== RESULTS FILE ====
    % Usage: [sStudy, iStudy, iResult] = bst_get('ResultsFile', ResultsFile, iStudies)
    %        [sStudy, iStudy, iResult] = bst_get('ResultsFile', ResultsFile)
    case 'ResultsFile'
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Input #2: ResultsFile
        ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        ResultsFile = varargin{2};
        ResultsFile = strrep(ResultsFile, ProtocolInfo.STUDIES, '');
        % Input #3: iStudies
        if (nargin < 3)
            iStudies = [];
        else
            iStudies = varargin{3};
        end
        % Look for surface file in all the surfaces of all subjects
        [argout1, argout2, argout3] = findFileInStudies('Result', 'FileName', ResultsFile, iStudies);
       
        
%% ==== RESULTS FOR DATA FILE ====
    % Usage: [sStudy, iStudy, iResults] = bst_get('ResultsForDataFile', DataFile)           : search the whole protocol
    % Usage: [sStudy, iStudy, iResults] = bst_get('ResultsForDataFile', DataFile, iStudies) : search only the specified studies
    case 'ResultsForDataFile'
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        % Input #2: DataFile
        DataFile = varargin{2};
        DataFile = strrep(DataFile, ProtocolInfo.STUDIES, '');
        % Determine in which studies to search for ResultsFile
        if (nargin >= 3)
            % Studies specified in argument
            iStudy = varargin{3};
        else
            % Get study in which DataFile is located
            [sStudy, iStudy] = bst_get('DataFile', DataFile);
            if isempty(iStudy)
                return;
            end
        end
        % Search selected studies
        [argout1, argout2, argout3] = findFileInStudies('Result', 'DataFile', DataFile, iStudy);


%% ==== STAT FILE ====
    % Usage: [sStudy, iStudy, iData] = bst_get('StatFile', StatFile, iStudies)
    %        [sStudy, iStudy, iData] = bst_get('StatFile', StatFile)
    case 'StatFile'
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Input #2: SataFile
        ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        StatFile = varargin{2};
        StatFile = strrep(StatFile, ProtocolInfo.STUDIES, '');
        % Input #3: iStudies
        if (nargin < 3)
            iStudies = [];
        else
            iStudies = varargin{3};
        end
        % Look for surface file in all the surfaces of all subjects
        [argout1, argout2, argout3] = findFileInStudies('Stat', 'FileName', StatFile, iStudies);
        
        
%% ==== STAT FOR DATA FILE ====
    % Usage: [sStudy, iStudy, iResults] = bst_get('StatForDataFile', DataFile)           : search the whole protocol
    % Usage: [sStudy, iStudy, iResults] = bst_get('StatForDataFile', DataFile, iStudies) : search only the specified studies
    case 'StatForDataFile'
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        % Parse inputs
        if (nargin >= 2)
            DataFile = varargin{2};
            DataFile = strrep(DataFile, ProtocolInfo.STUDIES, '');
        else
            error('Invalid call to bst_get().');
        end
        % Determine in which studies to search for ResultsFile
        if (nargin >= 3)
            % Studies specified in argument
            iStudies = varargin{3};
        else
            % Get study in which DataFile is located
            [sStudies, iStudies] = bst_get('DataFile', DataFile);
            if isempty(iStudies)
                return;
            end
        end
        % Search selected studies
        [argout1, argout2, argout3] = findFileInStudies('Stat', 'DataFile', DataFile, iStudies);
     
%% ==== TIMEFREQ FILE ====
    % Usage: [sStudy, iStudy, iTimefreq] = bst_get('TimefreqFile', TimefreqFile, iStudies)
    %        [sStudy, iStudy, iTimefreq] = bst_get('TimefreqFile', TimefreqFile)
    case 'TimefreqFile'
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Input #2: TimefreqFile
        ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        TimefreqFile = varargin{2};
        TimefreqFile = strrep(TimefreqFile, ProtocolInfo.STUDIES, '');
        % Remove optional RefRowName
        iPipe = find(TimefreqFile == '|', 1);
        if ~isempty(iPipe)
            TimefreqFile = TimefreqFile(1:iPipe-1);
        end
        % Input #3: iStudies
        if (nargin < 3)
            iStudies = [];
        else
            iStudies = varargin{3};
        end
        % Look for surface file in all the surfaces of all subjects
        [argout1, argout2, argout3] = findFileInStudies('Timefreq', 'FileName', TimefreqFile, iStudies);
        
%% ==== TIMEFREQ FOR FILE ====
    % Usage: [sStudy, iStudy, iTimefreq] = bst_get('TimefreqForFile', FileName, iStudies) : search only the specified studies
    %        [sStudy, iStudy, iTimefreq] = bst_get('TimefreqForFile', FileName)           : search the whole protocol
    case 'TimefreqForFile'
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        % Parse inputs
        if (nargin >= 2)
            FileName = varargin{2};
            FileName = strrep(FileName, ProtocolInfo.STUDIES, '');
        else
            error('Invalid call to bst_get().');
        end
        % Get study in which file is located
        if (nargin >= 3)
            iStudies = varargin{3};
            [sStudy, iStudy, iFile, DataType] = bst_get('AnyFile', FileName, iStudies);
        else
            [sStudy, iStudy, iFile, DataType] = bst_get('AnyFile', FileName);
        end
        % If file was not found
        if isempty(iStudy)
            return;
        end
        % Search direct dependent files
        [tmp, tmp, iTf] = findFileInStudies('Timefreq', 'DataFile', FileName, iStudy);
        % Data files: get all the depending results, and then all the timefreq for those results
        if strcmpi(DataType, 'data')
            [tmp, tmp, iResults] = bst_get('ResultsForDataFile', FileName, iStudy);
            for i = 1:length(iResults);
                % Search selected studies
                [tmp, tmp, iTfRes] = findFileInStudies('Timefreq', 'DataFile', sStudy.Result(iResults(i)).FileName, iStudy);
                if ~isempty(iTfRes)
                    iTf = [iTf iTfRes];
                end
            end
        end
        % Return results
        if ~isempty(iTf)
            argout1 = sStudy;
            argout2 = iStudy;
            argout3 = iTf;
        end
        
        
%% ==== DIPOLES FOR FILE ====
    % Usage: [sStudy, iStudy, iDipoles] = bst_get('DipolesForFile', FileName, iStudies) : search only the specified studies
    %        [sStudy, iStudy, iDipoles] = bst_get('DipolesForFile', FileName)           : search the whole protocol
    case 'DipolesForFile'
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        % Parse inputs
        if (nargin >= 2)
            FileName = varargin{2};
            FileName = strrep(FileName, ProtocolInfo.STUDIES, '');
        else
            error('Invalid call to bst_get().');
        end
        % Get study in which file is located
        if (nargin >= 3)
            iStudies = varargin{3};
            [sStudy, iStudy, iFile, DataType] = bst_get('AnyFile', FileName, iStudies);
        else
            [sStudy, iStudy, iFile, DataType] = bst_get('AnyFile', FileName);
        end
        % If file was not found
        if isempty(iStudy)
            return;
        end
        % Search direct dependent files
        [tmp, tmp, iDip] = findFileInStudies('Dipoles', 'DataFile', FileName, iStudy);
        % Data files: get all the depending results, and then all the timefreq for those results
        if strcmpi(DataType, 'data')
            [tmp, tmp, iResults] = bst_get('ResultsForDataFile', FileName, iStudy);
            for i = 1:length(iResults);
                % Search selected studies
                [tmp, tmp, iDipRes] = findFileInStudies('Dipoles', 'DataFile', sStudy.Result(iResults(i)).FileName, iStudy);
                if ~isempty(iDipRes)
                    iDip = [iDip, iDipRes];
                end
            end
        end
        % Return results
        if ~isempty(iDip)
            argout1 = sStudy;
            argout2 = iStudy;
            argout3 = iDip;
        end
        
        
%% ==== TIMEFREQ FOR KERNEL ====
    % Find all the timefreq files dependent from links due to a given kernel
    % Usage: [sStudy, iStudy, iTimefreq] = bst_get('TimefreqForKernel', KernelFile) 
    case 'TimefreqForKernel'
        sFoundStudy = [];
        iFoundStudy = [];
        iFoundTimefreq = [];
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Get study in which file is located
        KernelFile = varargin{2};
        [sStudy, iStudy, iFile, DataType] = bst_get('ResultsFile', KernelFile);
        if isempty(iStudy)
            return;
        end
        % Get all the data files relative with this kernel
        [iDepStudies, iDepDatas] = bst_get('DataForStudy', iStudy);
        % Keep only once each study
        iDepStudies = unique(iDepStudies);
        % Process all the dependent studies
        for iSt = 1:length(iDepStudies)
            % Get the study structure
            sDepStudy = bst_get('Study', iDepStudies(iSt));
            % Process each timefreq file separately
            for iTf = 1:length(sDepStudy.Timefreq)
                DataFile = sDepStudy.Timefreq(iTf).DataFile;
                % Keep only the files that are linked to LINKS
                if isempty(DataFile) || (length(DataFile) < 5) || ~isequal(DataFile(1:5), 'link|')
                    continue;
                end
                % Split link
                splitFile = str_split(DataFile, '|');
                % If the kernel is found: add it to the found list
                if file_compare(splitFile{2}, KernelFile)
                    sFoundStudy = [sFoundStudy sDepStudy];
                    iFoundStudy = [iFoundStudy, iDepStudies(iSt)];
                    iFoundTimefreq = [iFoundTimefreq, iTf];
                end
            end
        end
        % Return findings
        argout1 = sFoundStudy;
        argout2 = iFoundStudy;
        argout3 = iFoundTimefreq;
        
        
%% ==== DIPOLES FOR KERNEL ====
    % Find all the dipoles files dependent from links due to a given kernel
    % Usage: [sStudy, iStudy, iDipoles] = bst_get('TimefreqForKernel', KernelFile) 
    case 'DipolesForKernel'
        sFoundStudy = [];
        iFoundStudy = [];
        iFoundDipoles = [];
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Get study in which file is located
        KernelFile = varargin{2};
        [sStudy, iStudy, iFile, DataType] = bst_get('ResultsFile', KernelFile);
        if isempty(iStudy)
            return;
        end
        % Get all the data files relative with this kernel
        [iDepStudies, iDepDatas] = bst_get('DataForStudy', iStudy);
        % Keep only once each study
        iDepStudies = unique(iDepStudies);
        % Process all the dependent studies
        for iSt = 1:length(iDepStudies)
            % Get the study structure
            sDepStudy = bst_get('Study', iDepStudies(iSt));
            % Process each timefreq file separately
            for iDip = 1:length(sDepStudy.Dipoles)
                DataFile = sDepStudy.Dipoles(iDip).DataFile;
                % Keep only the files that are linked to LINKS
                if isempty(DataFile) || (length(DataFile) < 5) || ~isequal(DataFile(1:5), 'link|')
                    continue;
                end
                % Split link
                splitFile = str_split(DataFile, '|');
                % If the kernel is found: add it to the found list
                if file_compare(splitFile{2}, KernelFile)
                    sFoundStudy = [sFoundStudy sDepStudy];
                    iFoundStudy = [iFoundStudy, iDepStudies(iSt)];
                    iFoundDipoles = [iFoundDipoles, iDip];
                end
            end
        end
        % Return findings
        argout1 = sFoundStudy;
        argout2 = iFoundStudy;
        argout3 = iFoundDipoles;
        
        
%% ==== DIPOLES FILE ====
    % Usage: [sStudy, iStudy, iDipole] = bst_get('DipolesFile', DipolesFile, iStudies)
    %        [sStudy, iStudy, iDipole] = bst_get('DipolesFile', DipolesFile)
    case 'DipolesFile'
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Input #2: DipolesFile
        ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        DipolesFile = varargin{2};
        DipolesFile = strrep(DipolesFile, ProtocolInfo.STUDIES, '');
        % Input #3: iStudies
        if (nargin < 3)
            iStudies = [];
        else
            iStudies = varargin{3};
        end
        % Look for surface file in all the surfaces of all subjects
        [argout1, argout2, argout3] = findFileInStudies('Dipoles', 'FileName', DipolesFile, iStudies);
        
        
%% ==== MATRIX FILE ====
    % Usage: [sStudy, iStudy, iDipole] = bst_get('MatrixFile', MatrixFile, iStudies)
    %        [sStudy, iStudy, iDipole] = bst_get('MatrixFile', MatrixFile)
    case 'MatrixFile'
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Input #2: MatrixFile
        ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        MatrixFile = varargin{2};
        MatrixFile = strrep(MatrixFile, ProtocolInfo.STUDIES, '');
        % Input #3: iStudies
        if (nargin < 3)
            iStudies = [];
        else
            iStudies = varargin{3};
        end
        % Look for surface file in all the surfaces of all subjects
        [argout1, argout2, argout3] = findFileInStudies('Matrix', 'FileName', MatrixFile, iStudies);
        
%% ==== IMAGE FILE ====
    % Usage: [sStudy, iStudy, iDipole] = bst_get('ImageFile', ImageFile, iStudies)
    %        [sStudy, iStudy, iDipole] = bst_get('ImageFile', ImageFile)
    case 'ImageFile'
        % No protocol in database
        if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
            return;
        end
        % Input #2: ImageFile
        ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
        ImageFile = varargin{2};
        ImageFile = strrep(ImageFile, ProtocolInfo.STUDIES, '');
        % Input #3: iStudies
        if (nargin < 3)
            iStudies = [];
        else
            iStudies = varargin{3};
        end
        % Look for surface file in all the surfaces of all subjects
        [argout1, argout2, argout3] = findFileInStudies('Image', 'FileName', ImageFile, iStudies);
        
        
%% ==== ANY FILE ====
    % Usage: [sStudy, iStudy, iFile, DataType, sItem] = bst_get('AnyFile', FileName, iStudies)
    %        [sStudy, iStudy, iFile, DataType, sItem] = bst_get('AnyFile', FileName)
    case 'AnyFile'
        % Input #2: FileName
        FileName = varargin{2};
        if isempty(FileName)
            return
        end
        % Input #3: iStudies
        if (nargin < 3)
            iStudies = [];
        else
            iStudies = varargin{3};
        end
        % Get data format
        fileType = file_gettype(FileName);
        if isempty(fileType)
            error('File type is not recognized.');
        end
        sItem = [];
        % Get information related with this file
        switch (fileType)
            % ===== FUNCTIONAL =====
            case 'channel'
                [sStudy, iStudy] = bst_get('ChannelFile', FileName);
                iItem = 1;
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy.Channel;
                end
            case 'headmodel'
                [sStudy, iStudy, iItem] = bst_get('HeadModelFile', FileName);
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy.HeadModel(iItem);
                end
            case 'noisecov'
                [sStudy, iStudy, iItem] = bst_get('NoiseCovFile', FileName);
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy.NoiseCov(iItem);
                end
            case 'ndatacov'
                [sStudy, iStudy, iItem] = bst_get('DataCovFile', FileName);
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy.NoiseCov(iItem);
                end
            case 'data'
                [sStudy, iStudy, iItem] = bst_get('DataFile', FileName, iStudies);
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy.Data(iItem);
                end
            case {'results', 'link'}
                [sStudy, iStudy, iItem] = bst_get('ResultsFile', FileName, iStudies);
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy.Result(iItem);
                end
            case {'presults', 'pdata','ptimefreq','pmatrix'}
                [sStudy, iStudy, iItem] = bst_get('StatFile', FileName, iStudies);
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy.Stat(iItem);
                end
            case 'dipoles'
                [sStudy, iStudy, iItem] = bst_get('DipolesFile', FileName, iStudies);
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy.Dipoles(iItem);
                end
            case 'timefreq'
                % Remove optional RefRowName
                iPipe = find(FileName == '|', 1);
                if ~isempty(iPipe)
                    FileName = FileName(1:iPipe-1);
                end
                [sStudy, iStudy, iItem] = bst_get('TimefreqFile', FileName, iStudies);
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy.Timefreq(iItem);
                end
            case 'matrix'
                [sStudy, iStudy, iItem] = bst_get('MatrixFile', FileName, iStudies);
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy.Matrix(iItem);
                end
            case 'brainstormstudy'
                [sStudy, iStudy] = bst_get('Study', FileName);
                iItem = 0;
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy;
                end
            case {'image', 'video', 'videolink'}
                [sStudy, iStudy, iItem] = bst_get('ImageFile', FileName, iStudies);
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy.Image(iItem);
                end
            % ===== ANATOMY =====
            case {'cortex','scalp','innerskull','outerskull','tess','fibers','fem'}
                [sStudy, iStudy, iItem] = bst_get('SurfaceFile', FileName);
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy.Surface(iItem);
                end
            case 'subjectimage'
                [sStudy, iStudy, iItem] = bst_get('MriFile', FileName);
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy.Anatomy(iItem);
                end
            case 'brainstormsubject'
                [sStudy, iStudy] = bst_get('Subject', FileName);
                iItem = 0;
                if (nargout >= 5) && ~isempty(sStudy)
                    sItem = sStudy;
                end
            otherwise
                error('File type is not recognized.');
        end 
        argout1 = sStudy;
        argout2 = iStudy;
        argout3 = iItem;
        argout4 = fileType;
        if (nargout >= 5)
            argout5 = sItem;
        end
       
        
%% ==== GET RELATED DATA FILE ====
    % Usage: DataFile = bst_get('RelatedDataFile', FileName, iStudies)
    %        DataFile = bst_get('RelatedDataFile', FileName)
    case 'RelatedDataFile'
        % Input #2: FileName
        FileName = varargin{2};
        % Input #3: iStudies
        if (nargin < 3)
            iStudies = [];
        else
            iStudies = varargin{3};
        end
        % Get file in database
        [sStudy, iStudy, iFile, fileType] = bst_get('AnyFile', FileName, iStudies);
        % If this data file does not belong to any study
        if isempty(sStudy)
            return;
        end
        % Get associated data file
        switch (fileType)
            case 'data'
                RelatedDataFile = sStudy.Data(iFile).FileName;
            case {'pdata','presults','ptimefreq','pmatrix'}
                RelatedDataFile = sStudy.Stat(iFile).DataFile;
            case {'results', 'link'}
                RelatedDataFile = sStudy.Result(iFile).DataFile;
            case 'dipoles'
                RelatedDataFile = sStudy.Dipoles(iFile).DataFile;
            case 'timefreq'
                RelatedDataFile = sStudy.Timefreq(iFile).DataFile;
            otherwise
                RelatedDataFile = '';
        end
        % If related file is results: get related data file
        if ~isempty(RelatedDataFile)
            relFileType = file_gettype(RelatedDataFile);
            if ismember(relFileType, {'link','results'})
                RelatedDataFile = bst_get('RelatedDataFile', RelatedDataFile, iStudy);
            end
        end
        % Return file
        argout1 = RelatedDataFile;
        
%% ==== ALL CONDITIONS FOR ONE SUBJECT ====
    % Usage: [Conditions] =  bst_get('ConditionsForSubject', SubjectFile)
    case 'ConditionsForSubject'
        % Parse inputs
        if (nargin == 2)
            SubjectFile = varargin{2};
        else
            error('Invalid call to bst_get().');
        end
        % Get list of studies associated with subject
        sStudies = bst_get('StudyWithSubject', SubjectFile);
        % Get Conditions for each study
        Conditions = {};
        for i = 1:length(sStudies)
            % Test if the condition of this study was not added previously
            isNewCondition = 1;
            for iCond = 1:length(Conditions)
                % If new condition is found 
                % (and excludes DirAnalysisIntra and DirDefaultSubject from list)
                if isempty(sStudies(i).Condition) || ...
                   isequal(sStudies(i).Condition, Conditions(iCond)) || ...
                   strcmpi(sStudies(i).Condition{1}, bst_get('DirAnalysisIntra')) || ...
                   strcmpi(sStudies(i).Condition{1}, bst_get('DirDefaultSubject'))
                    isNewCondition = 0;
                    break;
                end
            end
            % If Condition is not added yet : add it to the list
            if isNewCondition && ~isempty(sStudies(i).Condition)
                Conditions{end+1} = sStudies(i).Condition{1};
            end
        end
        % Return conditions list
        argout1 = Conditions;
        
        
%% ==== ANATOMY DEFAULTS ====
    % Returns the list of all the anatomy defaults (distributed with the software + user defined)
    case 'AnatomyDefaults'
        % Parse inputs
        if (nargin == 2)
            AnatName = varargin{2};
        else
            AnatName = [];
        end
        % Get templates from the brainstorm3 folder
        progDir   = bst_fullfile(bst_get('BrainstormDefaultsDir'), 'anatomy');
        progFiles = dir(progDir);
        % Get templates from the user folder
        userDir   = bst_fullfile(bst_get('UserDefaultsDir'), 'anatomy');
        userFiles = dir(userDir);
        % Combine the two lists
        AllFiles = cat(2, cellfun(@(c)bst_fullfile(progDir,c), {progFiles.name}, 'UniformOutput', 0), ...
                          cellfun(@(c)bst_fullfile(userDir,c), setdiff({userFiles.name}, {progFiles.name}), 'UniformOutput', 0));
        % Initialize list of defaults
        sTemplates = repmat(struct('FilePath',[],'Name',[]), 0);
        % Find all the valid defaults (.zip files or subdirectory with a brainstormsubject.mat in it)
        for i = 1:length(AllFiles)
            % Decompose file name
            [fPath, fBase, fExt] = bst_fileparts(AllFiles{i});
            % Entry is a directory W/ a name that does not start with a '.' 
            if isempty(fBase) || strcmpi(fBase(1),'.') || (~isempty(fExt) && ~strcmpi(fExt, '.zip'))
                continue;
            end
            % If it's a folder: check for a brainstormsubject file
            if isdir(AllFiles{i})
                bstFiles = dir(bst_fullfile(AllFiles{i}, 'brainstormsubject*.mat'));
                if (length(bstFiles) == 1)
                    sTemplates(end+1).FilePath = AllFiles{i};
                    sTemplates(end).Name = fBase;
                end
            % If it's a zip file
            elseif isequal(fExt, '.zip')
                sTemplates(end+1).FilePath = AllFiles{i};
                sTemplates(end).Name = fBase;
            end
        end
        % Get defaults from internet 
        if ~ismember('icbm152', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=ICBM152_2019';
            sTemplates(end).Name = 'ICBM152';
        end
        if ~ismember('icbm152_2019', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=ICBM152_2019';
            sTemplates(end).Name = 'ICBM152_2019';
        end
        if ~ismember('icbm152_brainsuite_2016', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=ICBM152_BrainSuite_2016';
            sTemplates(end).Name = 'ICBM152_BrainSuite_2016';
        end
        if ~ismember('colin27_2016', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Colin27_2016';
            sTemplates(end).Name = 'Colin27_2016';
        end
        if ~ismember('colin27_brainsuite_2016', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Colin27_BrainSuite_2016';
            sTemplates(end).Name = 'Colin27_BrainSuite_2016';
        end
        if ~ismember('bci-dni_brainsuite_2020', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=BCI-DNI_BrainSuite_2020';
            sTemplates(end).Name = 'BCI-DNI_BrainSuite_2020';
        end
        if ~ismember('uscbrain_brainsuite_2020', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=USCBrain_BrainSuite_2020';
            sTemplates(end).Name = 'USCBrain_BrainSuite_2020';
        end
        if ~ismember('fsaverage_2020', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=FSAverage_2020';
            sTemplates(end).Name = 'FsAverage_2020';
        end
        if ~ismember('kabdebon_7w', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Kabdebon_7w';
            sTemplates(end).Name = 'Kabdebon_7w';
        end
        if ~ismember('oreilly_0.5m', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_0.5m';
            sTemplates(end).Name = 'Oreilly_0.5m';
        end
        if ~ismember('oreilly_1m', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_1m';
            sTemplates(end).Name = 'Oreilly_1m';
        end
        if ~ismember('oreilly_2m', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_2m';
            sTemplates(end).Name = 'Oreilly_2m';
        end
        if ~ismember(lower({sTemplates.Name}), 'oreilly_3m')
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_3m';
            sTemplates(end).Name = 'Oreilly_3m';
        end
        if ~ismember('oreilly_4.5m', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_4.5m';
            sTemplates(end).Name = 'Oreilly_4.5m';
        end
        if ~ismember('oreilly_6m', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_6m';
            sTemplates(end).Name = 'Oreilly_6m';
        end
        if ~ismember('oreilly_7.5m', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_7.5m';
            sTemplates(end).Name = 'Oreilly_7.5m';
        end
        if ~ismember('oreilly_9m', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_9m';
            sTemplates(end).Name = 'Oreilly_9m';
        end
        if ~ismember('oreilly_10.5m', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_10.5m';
            sTemplates(end).Name = 'Oreilly_10.5m';
        end
        if ~ismember('oreilly_12m', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_12m';
            sTemplates(end).Name = 'Oreilly_12m';
        end
        if ~ismember('oreilly_15m', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_15m';
            sTemplates(end).Name = 'Oreilly_15m';
        end
        if ~ismember('oreilly_18m', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_18m';
            sTemplates(end).Name = 'Oreilly_18m';
        end
        if ~ismember('oreilly_24m', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_24m';
            sTemplates(end).Name = 'Oreilly_24m';
        end
        % If a specific template was requested
        if ~isempty(AnatName)
            iAnat = find(strcmpi({sTemplates.Name}, AnatName));
            sTemplates = sTemplates(iAnat);
        end
        % Sort in alphabetical order
        if ~isempty(sTemplates)
            [tmp__, I] = sort_nat({sTemplates(2:end).Name});
            sTemplates = sTemplates([1, I+1]);
        end
        % Return defaults list
        argout1 = sTemplates;
        
        
%% ==== MNI ATLASES ====
    % Returns the list of all the available MNI atlases
    case 'MniAtlasDefaults'
        % Get templates from the brainstorm3 folder
        mniDir   = bst_fullfile(bst_get('UserDefaultsDir'), 'mniatlas');
        mniFiles = dir(bst_fullfile(mniDir, '*.nii.gz'));
        mniFiles = cellfun(@(c)bst_fullfile(mniDir,c), {mniFiles.name}, 'UniformOutput', 0);
        % Initialize list of defaults
        sTemplates = repmat(struct('FilePath',[],'Name',[],'Info',[]), 0);
        % Find all the valid defaults (.zip files or subdirectory with a brainstormsubject.mat in it)
        for i = 1:length(mniFiles)
            % Decompose file name
            [fPath, fBase, fExt] = bst_fileparts(mniFiles{i});
            % Keep only files with .nii and .nii.gz extensions
            if ~isempty(fBase) && (fBase(1) ~= '.') && ~isempty(fExt) && strcmpi(fExt, '.gz')
                sTemplates(end+1).FilePath = mniFiles{i};
                sTemplates(end).Name = strrep(fBase, '.nii', '');
                sTemplates(end).Info = '';
            end
        end
        % Sort in alphabetical order
        if ~isempty(sTemplates)
            [tmp__, I] = sort_nat(lower({sTemplates.Name}));
            sTemplates = sTemplates(I);
        end
        
        % Get defaults from internet
        if ~ismember('aal2', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_AAL2';
            sTemplates(end).Name = 'AAL2';
            sTemplates(end).Info = 'https://www.gin.cnrs.fr/en/tools/aal/';
        end
        if ~ismember('aal3', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_AAL3';
            sTemplates(end).Name = 'AAL3';
            sTemplates(end).Info = 'https://www.gin.cnrs.fr/en/tools/aal/';
        end
        if ~ismember('aicha', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_AICHA';
            sTemplates(end).Name = 'AICHA';
            sTemplates(end).Info = 'https://www.gin.cnrs.fr/en/tools/aicha';
        end
        if ~ismember('brainnetome', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Brainnetome';
            sTemplates(end).Name = 'Brainnetome';
            sTemplates(end).Info = 'http://atlas.brainnetome.org/';
        end
        if ~ismember('brainnetome_leaddbs', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Brainnetome_leaddbs';
            sTemplates(end).Name = 'Brainnetome_leaddbs';
            sTemplates(end).Info = 'http://atlas.brainnetome.org/';
        end
        if ~ismember('brodmann', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Brodmann';
            sTemplates(end).Name = 'Brodmann';
            sTemplates(end).Info = 'https://people.cas.sc.edu/rorden/mricro/lesion.html#brod';
        end
        if ~ismember('hammers83', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Hammers';
            sTemplates(end).Name = 'Hammers';
            sTemplates(end).Info = 'http://brain-development.org/brain-atlases/adult-brain-atlases/';
        end
        if ~ismember('neuromorphometrics', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Neuromorphometrics';
            sTemplates(end).Name = 'Neuromorphometrics';
            sTemplates(end).Info = 'https://search.kg.ebrains.eu/instances/Dataset/ef48c5e9-6b3c-4d5a-a9a9-e678fe10bdf6';
        end
        if ~ismember('julich-brain-v25', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Julich-Brain-v25';
            sTemplates(end).Name = 'Julich-Brain-v25';
            sTemplates(end).Info = 'https://search.kg.ebrains.eu/instances/Dataset/ef48c5e9-6b3c-4d5a-a9a9-e678fe10bdf6';
        end
        if ~ismember('schaefer2018_100_7net', lower({sTemplates.Name}))
            sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Schaefer2018';
            sTemplates(end).Name = 'Schaefer2018';
            sTemplates(end).Info = 'https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal';
        end
        % Return defaults list
        argout1 = sTemplates;
        
        
%% ==== EEG DEFAULTS ====
    % Returns an array of struct(fullpath, name) of all the Brainstorm eeg nets defaults
    % Usage: EegDefaults = bst_get('EegDefaults')
    %        EegDefaults = bst_get('EegDefaults', TemplateName=[], SetupName=[])
    case 'EegDefaults'
        % Parse inputs
        if (nargin >= 3)
            SetupName = varargin{3};
        else
            SetupName = [];
        end
        if (nargin >= 2)
            TemplateName = varargin{2};
        else
            TemplateName = [];
        end
        % Get templates from the brainstorm3 folder
        progDir   = bst_fullfile(bst_get('BrainstormDefaultsDir'), 'eeg');
        progFiles = dir(bst_fullfile(progDir, '*'));
        % Get templates from the user folder
        userDir   = bst_fullfile(bst_get('UserDefaultsDir'), 'eeg');
        userFiles = dir(bst_fullfile(userDir, '*'));
        % Combine the two lists
        dirList = cat(2, cellfun(@(c)bst_fullfile(progDir,c), {progFiles.name}, 'UniformOutput', 0), ...
                          cellfun(@(c)bst_fullfile(userDir,c), setdiff({userFiles.name}, {progFiles.name}), 'UniformOutput', 0));
        % Initialize list of folders
        fullDefaultsList = repmat(struct('contents','', 'name',''), 0);
        % For each template directory
        for iDir = 1:length(dirList)
            % Decompose file name
            [fPath, fBase, fExt] = bst_fileparts(dirList{iDir});
            % Entry is a not a folder, or starts with a "."
            if ~isdir(dirList{iDir}) || isempty(fBase) || strcmpi(fBase(1),'.')
                continue;
            end
            % Skip if it is not the requested template
            if ~isempty(TemplateName) && ~strcmpi(fBase, TemplateName)
                continue;
            end
            % Get files list
            fileList = dir(bst_fullfile(dirList{iDir}, 'channel*.mat'));
            defaultsList = repmat(struct('fullpath','', 'name',''), 0);
            % Find all the valid defaults (channel files)
            for iFile = 1:length(fileList)
                [tmp__, baseName] = bst_fileparts(fileList(iFile).name);
                baseName = strrep(baseName, 'channel_', '');
                baseName = strrep(baseName, '_channel', '');
                baseName = strrep(baseName, '_', ' ');
                % Skip if it is not the requested template
                if ~isempty(SetupName) && ~strcmpi(baseName, SetupName)
                    continue;
                end
                % Add to list of templates
                iNewDefault = length(defaultsList) + 1;
                defaultsList(iNewDefault).fullpath = bst_fullfile(dirList{iDir}, fileList(iFile).name);
                defaultsList(iNewDefault).name = baseName;
            end
            % Add files list to defaults list
            if ~isempty(defaultsList)
                 fullDefaultsList(end + 1) = struct('contents', defaultsList, ...
                                                    'name',     fBase);
            end
        end
        % Return defaults list
        argout1 = fullDefaultsList;
        
        
%% ==== GET FILENAMES ====
    case 'GetFilenames'
        iStudies = varargin{2};
        iItems = varargin{3};
        DataType = varargin{4};
        FileNames = cell(1, length(iStudies));
        argout1 = {};
        for i = 1:length(iStudies)
            % Get study definition
            sStudy = bst_get('Study', iStudies(i));
            if isempty(sStudy)
                continue;
            end
            % Recordings or sources
            switch (DataType)
                case 'data'
                    if (iItems(i) > length(sStudy.Data))
                        return;
                    end
                    FileNames{i} = sStudy.Data(iItems(i)).FileName;
                case 'results'
                    if (iItems(i) > length(sStudy.Result))
                        return;
                    end
                    FileNames{i} = sStudy.Result(iItems(i)).FileName;
                case 'timefreq'
                    if (iItems(i) > length(sStudy.Timefreq))
                        return;
                    end
                    FileNames{i} = sStudy.Timefreq(iItems(i)).FileName;
                case 'matrix'
                    if (iItems(i) > length(sStudy.Matrix))
                        return;
                    end
                    FileNames{i} = sStudy.Matrix(iItems(i)).FileName;
                case {'pdata','presults','ptimfreq'}
                    if (iItems(i) > length(sStudy.Stat))
                        return;
                    end
                    FileNames{i} = sStudy.Stat(iItems(i)).FileName;
            end
        end
        argout1 = FileNames;

        
%% ==== GUI ====
    case 'BstFrame'
        if isempty(GlobalData) || isempty(GlobalData.Program.GUI) || isempty(GlobalData.Program.GUI.mainWindow)
            argout1 = [];
        else
            argout1 = GlobalData.Program.GUI.mainWindow.jBstFrame;
        end
    case 'BstControls'
        if isempty(GlobalData) || isempty(GlobalData.Program) || isempty(GlobalData.Program.GUI) || isempty(GlobalData.Program.GUI.mainWindow)
            argout1 = [];
        else
            argout1 = GlobalData.Program.GUI.mainWindow;
        end
    case 'isGUI'
        if isempty(GlobalData) || isempty(GlobalData.Program) || ~isfield(GlobalData.Program, 'GuiLevel')
            argout1 = [];
        else
            argout1 = (GlobalData.Program.GuiLevel >= 1);
        end
    case 'GuiLevel'
        if isempty(GlobalData) || isempty(GlobalData.Program) || ~isfield(GlobalData.Program, 'GuiLevel')
            argout1 = [];
        else
            argout1 = GlobalData.Program.GuiLevel;
        end
    case 'ScreenDef'
        if isempty(GlobalData) || isempty(GlobalData.Program) || ~isfield(GlobalData.Program, 'ScreenDef')
            argout1 = [];
        else
            argout1 = GlobalData.Program.ScreenDef;
        end
    case 'DecorationSize'
        if isempty(GlobalData) || isempty(GlobalData.Program) || ~isfield(GlobalData.Program, 'DecorationSize')
            argout1 = [];
        else
            argout1 = GlobalData.Program.DecorationSize;
        end
    case 'Layout'
        % Default or current layout structure
        if ~isfield(GlobalData, 'Preferences') || ~isfield(GlobalData.Preferences, 'Layout') || ~((nargin == 1) || isfield(GlobalData.Preferences.Layout, varargin{2})) || ~isfield(GlobalData.Preferences.Layout, 'MainWindowPos')
            GlobalData.Preferences.Layout = db_template('Layout');
        end
        % Structure or property call
        if (nargin == 2) && ischar(varargin{2}) && isfield(GlobalData.Preferences.Layout, varargin{2})
            argout1 = GlobalData.Preferences.Layout.(varargin{2});
        elseif (nargin == 1)
            argout1 = GlobalData.Preferences.Layout;
        else
            error('Invalid call to bst_get.');
        end

    case 'ByteOrder'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ByteOrder')
            argout1 = GlobalData.Preferences.ByteOrder;
        else
            argout1 = 'l';
        end

    case 'UniformizeTimeSeriesScales'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'UniformizeTimeSeriesScales')
            argout1 = GlobalData.Preferences.UniformizeTimeSeriesScales;
        else
            argout1 = 1;
        end 
        
    case 'FlipYAxis'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'FlipYAxis')
            argout1 = GlobalData.Preferences.FlipYAxis;
        else
            argout1 = 0;
        end 
        
    case 'AutoScaleY'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'AutoScaleY')
            argout1 = GlobalData.Preferences.AutoScaleY;
        else
            argout1 = 1;
        end
        
    case 'ShowXGrid'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ShowXGrid')
            argout1 = GlobalData.Preferences.ShowXGrid;
        else
            argout1 = 0;
        end 
        
    case 'ShowYGrid'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ShowYGrid')
            argout1 = GlobalData.Preferences.ShowYGrid;
        else
            argout1 = 0;
        end
        
    case 'ShowZeroLines'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ShowZeroLines')
            argout1 = GlobalData.Preferences.ShowZeroLines;
        else
            argout1 = 1;
        end
        
    case 'Resolution'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'Resolution')
            argout1 = GlobalData.Preferences.Resolution;
        else
            argout1 = [0 0];
        end 
        
    case 'FixedScaleY'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'FixedScaleY') && isfield(GlobalData.Preferences.FixedScaleY, varargin{2}) && ~isempty(GlobalData.Preferences.FixedScaleY.(varargin{2}))
            argout1 = GlobalData.Preferences.FixedScaleY.(varargin{2});
        else
            argout1 = [];
        end
        
    case 'XScale'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'XScale')
            argout1 = GlobalData.Preferences.XScale;
        else
            argout1 = 'linear';
        end
        
    case 'YScale'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'YScale')
            argout1 = GlobalData.Preferences.YScale;
        else
            argout1 = 'linear';
        end        
        
    case 'ShowEventsMode'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ShowEventsMode')
            argout1 = GlobalData.Preferences.ShowEventsMode;
        else
            argout1 = 'dot';
        end

    case 'AutoUpdates'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'AutoUpdates')
            argout1 = GlobalData.Preferences.AutoUpdates;
        else
            argout1 = 1;
        end 
        
    case 'ForceMatCompression'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ForceMatCompression')
            argout1 = GlobalData.Preferences.ForceMatCompression;
        else
            argout1 = 0;
        end 
        
    case 'IgnoreMemoryWarnings'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'IgnoreMemoryWarnings')
            argout1 = GlobalData.Preferences.IgnoreMemoryWarnings;
        else
            argout1 = 0;
        end 
        
    case 'SystemCopy'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'SystemCopy')
            argout1 = GlobalData.Preferences.SystemCopy;
        else
            argout1 = 0;
        end
        
    case 'ExpertMode'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ExpertMode')
            argout1 = GlobalData.Preferences.ExpertMode;
        else
            argout1 = 0;
        end 
        
    case 'DisplayGFP'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'DisplayGFP')
            argout1 = GlobalData.Preferences.DisplayGFP;
        else
            argout1 = 1;
        end
        
    case 'DownsampleTimeSeries'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'DownsampleTimeSeries')
            if (GlobalData.Preferences.DownsampleTimeSeries == 1)
                GlobalData.Preferences.DownsampleTimeSeries = 5;
            end
            argout1 = GlobalData.Preferences.DownsampleTimeSeries;
        else
            argout1 = 5;
        end
        
    case 'GraphicsSmoothing'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'GraphicsSmoothing')
            argout1 = GlobalData.Preferences.GraphicsSmoothing;
        else
            argout1 = 5;
        end
        
    case 'DisableOpenGL'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'DisableOpenGL')
            argout1 = GlobalData.Preferences.DisableOpenGL;
        else
            argout1 = 0;
        end

    case 'InterfaceScaling'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'InterfaceScaling')
            argout1 = GlobalData.Preferences.InterfaceScaling;
        else
            % Get screen resolution
            if isfield(GlobalData, 'Program') && isfield(GlobalData.Program, 'ScreenDef') && isfield(GlobalData.Program.ScreenDef, 'javaPos') && ~isempty(GlobalData.Program.ScreenDef(1).javaPos)
                AvailableRes = [100 125 150 200 250 300 400];
                iRes = bst_closest(GlobalData.Program.ScreenDef(1).javaPos.width * 100 / 1920, AvailableRes);
                argout1 = AvailableRes(iRes);
            else
                argout1 = 100;
            end
        end
        
    case 'JOGLVersion'
        % If JOGL1 is available
        if exist('javax.media.opengl.GLCanvas', 'class')
            argout1 = 1;
        % If JOGL2 is available
        elseif exist('javax.media.opengl.awt.GLCanvas', 'class')
            argout1 = 2;
        % No JOGL available
        else
            argout1 = 0;
        end

    case 'TSDisplayMode'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'TSDisplayMode')
            argout1 = GlobalData.Preferences.TSDisplayMode;
        else
            argout1 = 'butterfly';
        end 

    case 'PluginCustomPath'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'PluginCustomPath') && ~isempty(GlobalData.Preferences.PluginCustomPath)
            argout1 = GlobalData.Preferences.PluginCustomPath;
        else
            argout1 = [];
        end
        
    case 'BrainSuiteDir'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'BrainSuiteDir') && ~isempty(GlobalData.Preferences.BrainSuiteDir)
            if isdir(GlobalData.Preferences.BrainSuiteDir) && file_exist(bst_fullfile(GlobalData.Preferences.BrainSuiteDir, 'bdp'))
                argout1 = GlobalData.Preferences.BrainSuiteDir;
            else
                argout1 = [];
            end
        else
            argout1 = [];
        end
        
    case 'SpmTpmAtlas'
        % Get template file
        tpmUser = bst_fullfile(bst_get('BrainstormUserDir'), 'defaults', 'spm', 'TPM.nii');
        if file_exist(tpmUser)
            argout1 = tpmUser;
            disp(['SPM12 template found: ' tpmUser]);
            return;
        end
        % If it does not exist: check in brainstorm3 folder
        tpmDistrib = bst_fullfile(bst_get('BrainstormHomeDir'), 'defaults', 'spm', 'TPM.nii');
        if file_exist(tpmDistrib)
            argout1 = tpmDistrib;
            disp(['SPM12 template found: ' tpmDistrib]);
            return;
        end
        % If it does not exist: check in spm12 folder
        PlugSpm = bst_plugin('GetInstalled', 'spm12');
        if ~isempty(PlugSpm)
            tpmSpm = bst_fullfile(PlugSpm.Path, PlugSpm.SubFolder, 'tpm', 'TPM.nii');
            if file_exist(tpmSpm)
                argout1 = tpmSpm;
                disp(['SPM12 template found: ' tpmSpm]);
                return;
            end
        else
            tpmSpm = '';
        end
        % Not found...
        disp('SPM12 template not found in any of the following folders:');
        disp([' - ' tpmUser]);
        disp([' - ' tpmDistrib]);
        if ~isempty(tpmSpm)
            disp([' - ' tpmSpm]);
        end
        % Return the preferred location: .brainstorm/defaults/spm/TPM.nii
        argout1 = tpmUser;
        
    case 'PythonExe'
        % Get saved value
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'PythonExe') && ~isempty(GlobalData.Preferences.PythonExe)
            if file_exist(GlobalData.Preferences.PythonExe)
                argout1 = GlobalData.Preferences.PythonExe;
            else
                disp(['BST> Error: Python executable not found: ' GlobalData.Preferences.PythonExe]);
                argout1 = [];
            end
        else
            argout1 = [];
        end
        % If not defined in Brainstorm, but set in Matlab
        if isempty(argout1)
            [pyVer, PythonExe] = bst_python_ver();
            if ~isempty(PythonExe) && file_exist(PythonExe)
                disp(['BST> Found Python executable: ' PythonExe]);
                argout1 = PythonExe;
                bst_set('PythonExe', PythonExe);
            end
        end
        
    case 'ElectrodeConfig'
        % Get modality
        Modality = varargin{2};
        if isempty(Modality) || ~ismember(Modality, {'EEG','ECOG','SEEG','ECOG+SEEG'})
            disp(['GET> Invalid modality: ' Modality]);
            Modality = 'EEG';
        end
        % Value was saved previously
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ElectrodeConfig') && isfield(GlobalData.Preferences.ElectrodeConfig, Modality) && isfield(GlobalData.Preferences.ElectrodeConfig.(Modality), 'ContactDiameter')
            argout1 = GlobalData.Preferences.ElectrodeConfig.(Modality);
        % Get default value
        else
            switch (Modality)
                case 'EEG'
                    ElectrodeConfig.Type            = 'eeg';
                    ElectrodeConfig.ContactDiameter = 0.010;
                    ElectrodeConfig.ContactLength   = 0.002;
                    ElectrodeConfig.ElecDiameter    = [];
                    ElectrodeConfig.ElecLength      = [];
                case 'ECOG'
                    ElectrodeConfig.Type            = 'ecog';
                    ElectrodeConfig.ContactDiameter = 0.004;
                    ElectrodeConfig.ContactLength   = 0.001;
                    ElectrodeConfig.ElecDiameter    = 0.0005;
                    ElectrodeConfig.ElecLength      = [];
                case {'SEEG','ECOG+SEEG'}
                    ElectrodeConfig.Type            = 'seeg';
                    ElectrodeConfig.ContactDiameter = 0.0008;
                    ElectrodeConfig.ContactLength   = 0.002;
                    ElectrodeConfig.ElecDiameter    = 0.0007;
                    ElectrodeConfig.ElecLength      = 0.070;
            end
            argout1 = ElectrodeConfig;
        end
        
    case 'UseSigProcToolbox'
        if isempty(GlobalData.Program.HasSigProcToolbox)
            % Check if Signal Processing Toolbox is installed
            GlobalData.Program.HasSigProcToolbox = exist('fir2', 'file') == 2;
        end
        % Return user preferences
        if ~GlobalData.Program.HasSigProcToolbox
            argout1 = 0;
        elseif isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'UseSigProcToolbox')
            argout1 = GlobalData.Preferences.UseSigProcToolbox;
        else
            argout1 = 1;
        end

    case 'CustomColormaps'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'CustomColormaps') && ~isempty(GlobalData.Preferences.CustomColormaps)
            argout1 = GlobalData.Preferences.CustomColormaps;
        else
            argout1 = repmat(struct('Name', '', 'CMap', []), 0);
        end
        
    case 'BFSProperties'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'BFSProperties') && ~isempty(GlobalData.Preferences.BFSProperties)
            argout1 = GlobalData.Preferences.BFSProperties;
        else
            argout1 = [.33 .0042 .33 .88 .93];
        end
        
    case 'LastUsedDirs'
        defPref = struct(...
            'ImportData',      '', ...
            'ImportChannel',   '', ...
            'ImportAnat',      '', ...
            'ImportMontage',   '', ...
            'ExportChannel',   '', ...
            'ExportData',      '', ...
            'ExportAnat',      '', ...
            'ExportProtocol',  '', ...
            'ExportImage',     '', ...
            'ExportScript',    '', ...
            'ExportMontage',   '');
        argout1 = FillMissingFields(contextName, defPref);
        % Check that all folders are valid
        fields = fieldnames(argout1);
        for i = 1:length(fields)
            if ~ischar(argout1.(fields{i})) || ~file_exist(argout1.(fields{i}))
                argout1.(fields{i}) = '';
            end
        end
        
    case 'DefaultFormats'
        defPref = struct(...
            'AnatIn',      'FreeSurfer', ...
            'ChannelIn',   '', ...
            'ChannelOut',  '', ...
            'DataIn',      'CTF', ...
            'DataOut',     '', ...
            'DipolesIn',   '', ...
            'DipolesOut',  '', ...
            'ImageOut',    '', ...
            'EventsIn',    '', ...
            'EventsOut',   '', ...
            'MriIn',       '', ...
            'MriOut',      'Nifti1', ...
            'NoiseCovIn',  '', ...
            'NoiseCovOut', '', ...
            'ResultsIn',   '', ...
            'ResultsOut',  '', ...
            'SpmOut',      '', ...
            'SspIn',       '', ...
            'SspOut',      '', ...
            'SurfaceIn',   '', ...
            'SurfaceOut',  '', ...
            'LabelIn',     '', ...
            'LabelOut',    '', ...
            'TimefreqIn',  '', ...
            'TimefreqOut', '', ...
            'MatrixIn',    '', ...
            'MatrixOut',   '', ...
            'MontageIn',   '', ...
            'MontageOut',  '', ...
            'FibersIn',    '');
        argout1 = FillMissingFields(contextName, defPref);

    case 'OsType'
        switch (mexext)
            case 'mexglx',    argout1 = 'linux32';
            case 'mexa64',    argout1 = 'linux64';
            case 'mexmaci',   argout1 = 'mac32';
            case 'mexmaci64', argout1 = 'mac64';
            case 'mexs64',    argout1 = 'sol64';
            case 'mexw32',    argout1 = 'win32';
            case 'mexw64',    argout1 = 'win64';
            otherwise,        error('Unsupported extension.');
        end
        % CALL: bst_get('OsType', isMatlab=0)
        if (nargin >= 2) && isequal(varargin{2}, 0)
            if strcmpi(argout1, 'win32') && (~isempty(strfind(java.lang.System.getProperty('java.home'), '(x86)')) || ~isempty(strfind(java.lang.System.getenv('ProgramFiles(x86)'), '(x86)')))
                argout1 = 'win64';
            end
        end
        
    case 'ImportDataOptions'
        defPref = db_template('ImportOptions');
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'RawViewerOptions'
        defPref =  struct(...
            'PageDuration',   3, ...
            'RemoveBaseline', 'all', ...
            'UseCtfComp',     1, ...
            'Shortcuts',      []);
        defPref.Shortcuts = {...
            '1', 'event1', 'simple', []; ...   % Key, event name, event type (simple,extended,page), epoch time
            '2', 'event2', 'simple', []; ... 
            '3', 'event3', 'simple', []; ...
            '4', 'event4', 'simple', []; ...
            '5', 'event5', 'simple', []; ...
            '6', 'event6', 'simple', []; ...
            '7', 'event7', 'simple', []; ...
            '8', 'event8', 'simple', []; ...
            '9', 'event9', 'simple', []};
        argout1 = FillMissingFields(contextName, defPref);
        % If invalid PageDuration: reset to default
        if (argout1.PageDuration <= 0.1)
            argout1.PageDuration = defPref.PageDuration;
        end
        % If old shortcuts: reset to defaults
        if any(size(argout1.Shortcuts) ~= size(defPref.Shortcuts))
            disp('BST> Warning: Reset keyboard shortcuts to include new options.');
            argout1.Shortcuts = defPref.Shortcuts;
            bst_set('RawViewerOptions', argout1);
        end

    case 'MontageOptions'
        defPref = struct('Shortcuts', []);
        defPref.Shortcuts = {
           %'a', []; ... Note: A is reserved for All channels
            'b', []; ...
            'c', []; ...
            'd', []; ...
            'e', []; ...
            'f', []; ...
            'g', []; ...
            'h', []; ...
            'i', []; ...
            'j', []; ...
            'k', []; ...
            'l', []; ...
            'm', []; ...
            'n', []; ...
            'o', []; ...
            'p', []; ...
            'q', []; ...
            'r', []; ...
            's', []; ...
            't', []; ...
            'u', []; ...
            'v', []; ...
            'w', []; ...
            'x', []; ...
            'y', []; ...
            'z', []; ...
            };
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'TopoLayoutOptions'
        defPref = struct(...
            'TimeWindow',      [], ...
            'WhiteBackground', 0, ...
            'ShowRefLines',    1, ...
            'ShowLegend',      1, ...
            'ContourLines',    10);
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'StatThreshOptions'
        defPref = struct(...
            'pThreshold',    .05, ...
            'durThreshold',  0, ...
            'Correction',    'fdr', ...
            'Control',       [1 2 3]);
        argout1 = FillMissingFields(contextName, defPref);
        % Make sure that Control is not a string (previous brainstorm version)
        if ischar(argout1.Control)
            argout1.Control = defPref.Control;
        end
        % Make sure that 'no' is used instead of 'none' (previous brainstorm version)
        if strcmpi(argout1.Correction, 'none')
            argout1.Correction = 'no';
        end
        
    case 'ContactSheetOptions'
        defPref = struct(...
            'nImages',    20, ...
            'TimeRange',  [], ...
            'SkipVolume', 0.2);
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'ProcessOptions'
        defPref = struct(...
            'SavedParam',    struct(), ...
            'MaxBlockSize',  100 / 8 * 1024 * 1024, ...   % 100Mb
            'LastMaxBlockSize',  100 / 8 * 1024 * 1024);  % 100Mb
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'ImportEegRawOptions'
        defPref = struct(...
            'isCanceled',        0, ...
            'BaselineDuration',  0, ...
            'SamplingRate',      1000, ...
            'MatrixOrientation', 'channelXtime', ... % {'channelXtime', 'timeXchannel'}
            'VoltageUnits',      'V', ...            % {'\muV', 'mV', 'V'}
            'SkipLines',         0, ...
            'nAvg',              1, ...
            'isChannelName',     0);                 % 1 if the first entry contains the channel name
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'BugReportOptions'
        defPref = struct(...
            'isEnabled',  0, ...
            'SmtpServer', 'mailhost.chups.jussieu.fr', ...
            'UserEmail',  '');
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'DefaultSurfaceDisplay'
        defPref = struct(...
            'SurfShowSulci',    1, ...
            'SurfSmoothValue',  0, ...
            'DataThreshold',    0.5, ...
            'SizeThreshold',    1, ...
            'DataAlpha',        0);
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'MagneticExtrapOptions'
        defPref = struct(...
            'ForceWhitening', 0, ...
            'EpsilonValue',   0.0001);
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'DefaultFreqBands'
        argout1 = {...
            'delta',  '2, 4',   'mean'; ...
            'theta',  '5, 7',   'mean'; ...
            'alpha',  '8, 12',  'mean'; ...
            'beta',   '15, 29', 'mean'; ...
            'gamma1', '30, 59', 'mean'; ...
            'gamma2', '60, 90', 'mean'};
        
    case 'TimefreqOptions_morlet'
        defPref.isTimeBands     = 0;
        defPref.isFreqBands     = 0;
        defPref.isFreqLog       = 0;
        defPref.TimeBands       = {};
        defPref.Freqs           = '1:1:60';
        defPref.FreqsLog        = '1:40:150';
        defPref.FreqBands       = bst_get('DefaultFreqBands');
        defPref.Measure         = 'power';
        defPref.SaveKernel      = 0;
        defPref.Output          = 'all';
        defPref.RemoveEvoked    = 0;
        defPref.ClusterFuncTime = 'after';
        defPref.MorletFc        = 1;
        defPref.MorletFwhmTc    = 3;
        argout1 = FillMissingFields(contextName, defPref);
        if isempty(argout1.Freqs)
            argout1.Freqs = defPref.Freqs;
        end
        if ~isempty(argout1.FreqBands) && ~ischar(argout1.FreqBands{1,2})
            argout1.FreqBands = defPref.FreqBands;
        end

    case 'TimefreqOptions_hilbert'
        defPref.isTimeBands     = 0;
        defPref.isFreqBands     = 1;
        defPref.isFreqLog       = 0;
        defPref.TimeBands       = {};
        defPref.Freqs           = [];
        defPref.FreqsLog        = [];
        defPref.FreqBands       = bst_get('DefaultFreqBands');
        defPref.Measure         = 'power';
        defPref.SaveKernel      = 0;
        defPref.Output          = 'all';
        defPref.RemoveEvoked    = 0;
        defPref.ClusterFuncTime = 'after';
        argout1 = FillMissingFields(contextName, defPref);
        if isempty(argout1.Freqs)
            argout1.Freqs = defPref.Freqs;
        end
        if ~isempty(argout1.FreqBands) && ~ischar(argout1.FreqBands{1,2})
            argout1.FreqBands = defPref.FreqBands;
        end
        
    case 'TimefreqOptions_plv'
        defPref.isTimeBands     = 0;
        defPref.isFreqBands     = 1;
        defPref.isFreqLog       = 0;
        defPref.TimeBands       = {};
        defPref.Freqs           = [];
        defPref.FreqsLog        = [];
        defPref.FreqBands       = bst_get('DefaultFreqBands');
        defPref.Measure         = 'other';
        defPref.SaveKernel      = 0;
        defPref.Output          = 'all';
        defPref.ClusterFuncTime = 'after';
        argout1 = FillMissingFields(contextName, defPref);
        if isempty(argout1.Freqs)
            argout1.Freqs = defPref.Freqs;
        end
        if ~isempty(argout1.FreqBands) && ~ischar(argout1.FreqBands{1,2})
            argout1.FreqBands = defPref.FreqBands;
        end
        
    case 'TimefreqOptions_fft'
        defPref.isTimeBands     = 0;
        defPref.isFreqBands     = 0;
        defPref.isFreqLog       = 0;
        defPref.TimeBands       = {};
        defPref.Freqs           = [];
        defPref.FreqsLog        = [];
        defPref.FreqBands       = bst_get('DefaultFreqBands');
        defPref.Measure         = 'power';
        defPref.Output          = 'all';
        defPref.ClusterFuncTime = 'after';
        argout1 = FillMissingFields(contextName, defPref);
        if isempty(argout1.Freqs)
            argout1.Freqs = defPref.Freqs;
        end
        if ~isempty(argout1.FreqBands) && ~ischar(argout1.FreqBands{1,2})
            argout1.FreqBands = defPref.FreqBands;
        end
        
    case 'TimefreqOptions_psd'
        defPref.isTimeBands     = 0;
        defPref.isFreqBands     = 0;
        defPref.isFreqLog       = 0;
        defPref.TimeBands       = {};
        defPref.Freqs           = [];
        defPref.FreqsLog        = [];
        defPref.FreqBands       = bst_get('DefaultFreqBands');
        defPref.Measure         = 'power';
        defPref.Output          = 'all';
        defPref.ClusterFuncTime = 'after';
        argout1 = FillMissingFields(contextName, defPref);
        if isempty(argout1.Freqs)
            argout1.Freqs = defPref.Freqs;
        end
        if ~isempty(argout1.FreqBands) && ~ischar(argout1.FreqBands{1,2})
            argout1.FreqBands = defPref.FreqBands;
        end
    
    case 'ExportBidsOptions'
        defPref.ProjName    = [];
        defPref.ProjID      = [];
        defPref.ProjDesc    = [];
        defPref.Categories  = [];
        defPref.JsonDataset = ['{' 10 '  "License": "PD"' 10 '}'];
        defPref.JsonMeg     = ['{' 10 '  "TaskDescription": "My task"' 10 '}'];
        argout1 = FillMissingFields(contextName, defPref);        
        
    case 'OpenMEEGOptions'
        defPref.BemFiles     = {};
        defPref.BemNames     = {'Scalp', 'Skull', 'Brain'};
        defPref.BemCond      = [1, 0.0125, 1];
        defPref.BemSelect    = [1 1 1];
        defPref.isAdjoint    = 0;
        defPref.isAdaptative = 1;
        defPref.isSplit      = 0;
        defPref.SplitLength  = 4000;
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'DuneuroOptions'
        defPref = duneuro_defaults();        
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'GridOptions_dipfit'
        defPref = struct(...
            'Method',         'isotropic', ...
            'nLayers',        17, ...
            'Reduction',      3, ...
            'nVerticesInit',  4000, ...
            'Resolution',     0.020, ...
            'FileName',       '');        
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'GridOptions_headmodel'
        defPref = struct(...
            'Method',         'isotropic', ...
            'nLayers',        17, ...
            'Reduction',      3, ...
            'nVerticesInit',  4000, ...
            'Resolution',     0.005, ...
            'FileName',       '');
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'MriOptions'
        defPref = struct(...
            'isRadioOrient',    0, ...
            'isMipAnatomy',     0, ...
            'isMipFunctional',  0, ...
            'OverlaySmooth',    0, ...
            'InterpDownsample', 3, ...
            'DistanceThresh',   6, ...
            'UpsampleImage',    0, ...
            'DefaultAtlas',     []);
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'DigitizeOptions'
        defPref = struct(...
            'ComPort',      'COM1', ...
            'ComRate',      9600, ...
            'ComByteCount', 94, ...  % 47 bytes * 2 receivers
            'UnitType',     'fastrak', ...
            'PatientId',    'S001', ...
            'nFidSets',     2, ...
            'isBeep',       1, ...
            'isMEG',        1, ...
            'isSimulate',   0, ...
            'Montages',     [...
                struct('Name',   'No EEG', ...
                       'Labels', []), ...
                struct('Name',   'Default', ...
                       'Labels', [])], ...
            'iMontage',     1);
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'NodelistOptions'
        defPref = struct(...
            'String', '', ...         % What to search for
            'Target', 'Comment', ...  % What field to search for: {'FileName', 'Comment'}
            'Action', 'Select');      % What to do with the filtered files: {'Select', 'Exclude'}
        argout1 = FillMissingFields(contextName, defPref);
        
    case 'ReadOnly'
        if isfield(GlobalData.DataBase, 'isReadOnly')
            argout1 = GlobalData.DataBase.isReadOnly;
        else
            argout1 = 0;
        end
        
    case 'LastPsdDisplayFunction'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'LastPsdDisplayFunction')
            argout1 = GlobalData.Preferences.LastPsdDisplayFunction;
        else
            argout1 = [];
        end

    case 'PlotlyCredentials'
        try
            creds = loadplotlycredentials();
            argout1 = creds.username;
            argout2 = creds.api_key;
        catch
            argout1 = '';
            argout2 = '';
        end
        
        try
            config = loadplotlyconfig();
            argout3 = config.plotly_domain;
        catch
            argout3 = '';
        end

    case 'KlustersExecutable'
        if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'KlustersExecutable')
            argout1 = GlobalData.Preferences.KlustersExecutable;
        else
            argout1 = [];
        end
        
        
%% ===== FILE FILTERS =====
    case 'FileFilters'
        switch lower(varargin{2})
            case 'mri'
                argout1 = {...
                    {'.img'},          'MRI: Analyze (*.img/*.hdr)',           'Analyze'; ...
                    {'.ima'},          'MRI: BrainVISA GIS (*.ima/*.dim)',     'GIS'; ...
                    {'.ima'},          'MRI: BrainVISA GIS (*.ima/*.dim)',     'GIS'; ...
                    {'.mri'},          'MRI: CTF (*.mri)',                     'CTF'; ...
                    {'.mat'},          'MRI: FieldTrip (*.mat)',               'FT-MRI'; ...
                    {'.mgh','.mgz'},   'MRI: MGH (*.mgh,*.mgz)',               'MGH'; ...
                    {'.mnc', '.mni'},  'MRI: MNI (*.mnc,*.mni)',               'MINC'; ...
                    {'.nii','.gz'},    'MRI: NIfTI-1 (*.nii;*.nii.gz)',        'Nifti1'; ...
                    {'_subjectimage'}, 'MRI: Brainstorm (*subjectimage*.mat)', 'BST'; ...
                    {'*'},             'MRI: DICOM (SPM converter)',           'DICOM-SPM'; ...
                    {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'All MRI files (subject space)', 'ALL'; ...
                    {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'All MRI files (MNI space)',     'ALL-MNI'; ...
                    {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'Volume atlas (subject space)',  'ALL-ATLAS'; ...
                    {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'Volume atlas (MNI space)',      'ALL-MNI-ATLAS'; ...
                   };
            case 'mriout'
                argout1 = {...
                    {'.img'}, 'MRI: Analyze (*.img/*.hdr)',         'Analyze'; ...
                    {'.ima'}, 'MRI: BrainVISA GIS (*.ima/*.dim)',   'GIS'; ...
                    {'.mri'}, 'MRI: CTF (*.mri)',                   'CTF'; ...
                    {'.mat'}, 'MRI: FieldTrip (*.mat)',             'FT-MRI'; ...
                    {'.nii'}, 'MRI: NIfTI-1 (*.nii)',               'Nifti1'...
                   };
            case 'anatin'
                argout1 = {...
                    {'.folder'}, 'FreeSurfer', 'FreeSurfer-fast'; ...
                    {'.folder'}, 'FreeSurfer + Volume atlases', 'FreeSurfer'; ...
                    {'.folder'}, 'FreeSurfer + Volume atlases + Thickness', 'FreeSurfer+Thick'; ...
                    {'.folder'}, 'BrainSuite', 'BrainSuite-fast'; ...
                    {'.folder'}, 'BrainSuite + Volume atlases', 'BrainSuite'; ...
                    {'.folder'}, 'BrainVISA', 'BrainVISA'; ...
                    {'.folder'}, 'CAT12', 'CAT12'; ...
                    {'.folder'}, 'CAT12 + Thickness', 'CAT12+Thick'; ...
                    {'.folder'}, 'CIVET', 'CIVET'; ...
                    {'.folder'}, 'CIVET + Thickness', 'CIVET+Thick'; ...
                    {'.folder'}, 'HCP MEG/anatomy (pipeline v3)', 'HCPv3'; ...
                    {'.folder'}, 'SimNIBS', 'SimNIBS'; ...
                   };
            case 'source4d'
                argout1 = {...
                    {'.folder'}, 'NIfTI-1 (*.nii)',                  'Nifti1';...
                    {'.folder'}, 'Analyze (*.img/*.hdr)',            'Analyze'; ...
                    {'.folder'}, 'Matlab 4D matrix (*voltime*.mat)', 'BST'; ...
                   };
                    
            case 'surface'
                argout1 = {...
                    {'.mesh'},  'BrainVISA (*.mesh)',      'MESH'; ...
                    {'_tess', '_head', '_scalp', '_brain', '_cortex', '_innerskull', '_outerskull'}, 'Brainstorm (*.mat)', 'BST'; ...
                    {'.dfs'},   'BrainSuite (*.dfs)',      'DFS'; ...
                    {'.dsgl'},  'BrainSuite old (*.dsgl)', 'DSGL'; ...
                    {'.bd0','.bd1','.bd2','.bd3','.bd4','.bd5','.bd6','.bd7','.bd8','.bd9', ...
                     '.s00','.s01','.s02','.s03','.s04','.s05','.s06','.s07','.s08','.s09'}, ...
                                'Curry BEM (*.db*;*.s0*)', 'CURRY-BEM';
                    {'.vtk'},   'FSL: VTK (*.vtk)',        'VTK'; ...
                    {'*'},      'FreeSurfer (*.*)',        'FS';
                    {'.off'},   'Geomview OFF (*.off)',    'OFF'; ...
                    {'.gii'},   'GIfTI / MRI coordinates (*.gii)', 'GII'; ...
                    {'.gii'},   'GIfTI / MNI coordinates (*.gii)', 'GII-MNI'; ...
                    {'.gii'},   'GIfTI / World coordinates (*.gii)', 'GII-WORLD'; ...
                    {'.fif'},   'MNE (*.fif)',             'FIF'; ...
                    {'.obj'},   'MNI OBJ (*.obj)',         'MNIOBJ'; ...
                    {'.msh'},   'SimNIBS Gmsh4 (*.msh)',   'SIMNIBS'; ...
                    {'.tri'},   'TRI (*.tri)',             'TRI'; ...
                    {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'Volume mask or atlas (subject space)', 'MRI-MASK'; ...
                    {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz'},                  'Volume mask or atlas (MNI space)',     'MRI-MASK-MNI'; ...
                    {'.nwbaux'},   'Neurodata Without Borders (*.nwbaux)', 'NWB'; ...
                    {'*'},      'All surface files (*.*)', 'ALL'; ...
                   };
               
            case 'surfaceout'
                argout1 = {...
                    {'.mesh'}, 'BrainVISA (*.mesh)',   'MESH'; ...
                    {'.dfs'},  'BrainSuite (*.dfs)',   'DFS'; ...
                    {'.fs'},   'FreeSurfer (*.fs)',    'FS'
                    {'.off'},  'Geomview OFF (*.off)', 'OFF'; ...
                    {'.gii'},  'GIfTI (*.gii)',        'GII'; ...
                    {'.tri'},  'TRI (*.tri)',          'TRI'; ...
                   };
                
            case 'data'
                argout1 = {...
                     {'.*'},                 'MEG/EEG: 4D-Neuroimaging/BTi (*.*)',   '4D'; ...
                     {'.meg4','.res4'},      'MEG/EEG: CTF (*.ds;*.meg4;*.res4)',    'CTF'; ...
                     {'.fif'},               'MEG/EEG: Elekta-Neuromag (*.fif)',     'FIF'; ...
                     {'.mat'},               'MEG/EEG: FieldTrip (*.mat)',           'FT-TIMELOCK'; ...
                     {'.raw'},               'MEG/EEG: ITAB (*.raw)',                'ITAB'; ...
                     {'.kdf'},               'MEG/EEG: KRISS MEG (*.kdf)',           'KDF'; ...
                     {'.mrk','.sqd','.con','.raw','.ave'},  'MEG/EEG: Ricoh (*.sqd;*.con;*.raw;*.ave;*.mrk)', 'RICOH'; ...
                     {'.mat'},               'MEG/EEG: SPM (*.mat/.dat)',            'SPM-DAT'; ...
                     {'.mrk','.sqd','.con','.raw','.ave'},  'MEG/EEG: Yokogawa/KIT (*.sqd;*.con;*.raw;*.ave;*.mrk)', 'KIT'; ...
                     {'.hdf5'},              'MEG/EEG: York Instruments MEGSCAN (.hdf5)', 'MEGSCAN-HDF5'; ...
                     {'.bst'},               'MEG/EEG: Brainstorm binary (*.bst)',   'BST-BIN'; ...
                     {'.adicht'},            'EEG: ADInstruments LabChart (*.adicht)', 'EEG-ADICHT'; ...
                     {'.msr'},               'EEG: ANT ASA (*.msr)',                 'EEG-ANT-MSR'; ...
                     {'.cnt','.avr'},        'EEG: ANT EEProbe (*.cnt;*.avr)',       'EEG-ANT-CNT'; ...
                     {'*'},                  'EEG: ASCII text (*.*)',                'EEG-ASCII'; ...
                     {'.bdf'},               'EEG: BDF (*.bdf)',                     'EEG-BDF'; ...
                     {'.avr','.mux','.mul'}, 'EEG: BESA exports (*.avr;*.mul;*.mux)', 'EEG-BESA'; ...
                     {'.ns1','.ns2','.ns3','.ns4','.ns5','.ns6'}, 'EEG: Blackrock NeuroPort (*.nsX/*.nev)', 'EEG-BLACKROCK';
                     {'.eeg','.dat'},        'EEG: BrainAmp (*.eeg;*.dat)',          'EEG-BRAINAMP'; ...
                     {'.txt'},               'EEG: BrainVision Analyzer (*.txt)',    'EEG-BRAINVISION'; ...
                     {'.sef','.ep','.eph'},  'EEG: Cartool (*.sef;*.ep;*.eph)',      'EEG-CARTOOL'; ...
                     {'.dat','.cdt'},        'EEG: Curry (*.dat;*.cdt)',             'EEG-CURRY'; ...
                     {'.smr','.son'},        'EEG: CED Spike2 old 32bit (*.smr;*.son)',  'EEG-SMR'; ...
                     {'.smr','.smrx'},       'EEG: CED Spike2 new 64bit (*.smr;*.smrx)', 'EEG-SMRX'; ...
                     {'.rda'},               'EEG: Compumedics ProFusion Sleep (*.rda)',  'EEG-COMPUMEDICS-PFS'; ...
                     {'.bin'},               'EEG: Deltamed Coherence-Neurofile (*.bin)', 'EEG-DELTAMED'; ...
                     {'.edf','.rec'},        'EEG: EDF / EDF+ (*.rec;*.edf)',        'EEG-EDF'; ...
                     {'.set'},               'EEG: EEGLAB (*.set)',                  'EEG-EEGLAB'; ...
                     {'.raw'},               'EEG: EGI Netstation RAW (*.raw)',      'EEG-EGI-RAW'; ...
                     {'.mff','.bin'},        'EEG: EGI-Philips (*.mff)',             'EEG-EGI-MFF'; ...
                     {'.edf'},               'EEG: EmotivPRO (*.edf)',               'EEG-EMOTIV'; ...
                     {'.erp','.hdr'},        'EEG: ERPCenter (*.hdr;*.erp)',         'EEG-ERPCENTER'; ...
                     {'.erp'},               'EEG: ERPLab (*.erp)',                  'EEG-ERPLAB'; ...
                     {'.mat','.hdf5'},       'EEG: g.tec Matlab (*.mat,*.hdf5)',     'EEG-GTEC'; ...
                     {'.rhd','.rhs'},        'EEG: Intan (*.rhd,*.rhs)',             'EEG-INTAN'; ...
                     {'.mb2'},               'EEG: MANSCAN (*.mb2)',                 'EEG-MANSCAN'; ...
                     {'.trc'},               'EEG: Micromed (*.trc)',                'EEG-MICROMED'; ...
                     {'.mat'},               'EEG: Matlab matrix (*.mat)',           'EEG-MAT'; ...
                     {'.csv'},               'EEG: Muse (*.csv)',                    'EEG-MUSE-CSV'; ...
                     {'.ncs'},               'EEG: Neuralynx (*.ncs)',               'EEG-NEURALYNX'; ...
                     {'.bin'},               'EEG: NeurOne session folder',          'EEG-NEURONE'; ...
                     {'.cnt','.avg','.eeg','.dat'}, 'EEG: Neuroscan (*.cnt;*.eeg;*.avg;*.dat)', 'EEG-NEUROSCAN'; ...
                     {'.eeg','.dat'},        'EEG: NeuroScope (*.eeg;*.dat)',        'EEG-NEUROSCOPE'; ...
                     {'.e'},                 'EEG: Nicolet (*.e)',                   'EEG-NICOLET'; ...
                     {'.eeg'},               'EEG: Nihon Kohden (*.eeg)',            'EEG-NK'; ...
                     {'.dat'},               'EEG: Open Ephys flat binary (*.dat)',  'EEG-OEBIN'; ...
                     {'.plx','.pl2'},        'EEG: Plexon (*.plx;*.pl2)',            'EEG-PLEXON'; ...
                     {'.ns1','.ns2','.ns3','.ns4','.ns5','.ns6'}, 'EEG: Ripple Trellis (*.nsX/*.nev)', 'EEG-RIPPLE'; ...
                     {'.h5'},                'EEG: The Virtual Brain (*_TimeSeriesEEG.h5)', 'EEG-TVB'; ...
                     {'.csv'},               'EEG: Wearable Sensing (*.csv)',        'EEG-WS-CSV'; ...
                     {'.nirs'},              'NIRS: Brainsight (*.nirs)',            'NIRS-BRS'; ...
                     {'.bnirs','.jnirs','.snirf'}, 'NIRS: SNIRF (*.snirf)',          'NIRS-SNIRF'; ...
                     {'.edf'},               'EyeLink eye tracker (*.edf)',          'EYELINK'; ...
                    };
            case 'raw'
                argout1 = {...
                     {'.*'},                 'MEG/EEG: 4D-Neuroimaging/BTi (*.*)',   '4D'; ...
                     {'.meg4','.res4'},      'MEG/EEG: CTF (*.ds;*.meg4;*.res4)',    'CTF'; ...
                     {'.fif'},               'MEG/EEG: Elekta-Neuromag (*.fif)',     'FIF'; ...
                     {'.mat'},               'MEG/EEG: FieldTrip (*.mat)',           'FT-TIMELOCK'; ...
                     {'.raw'},               'MEG/EEG: ITAB (*.raw)',                'ITAB'; ...
                     {'.kdf'},               'MEG/EEG: KRISS MEG (*.kdf)',           'KDF'; ...
                     {'.mrk','.sqd','.con','.raw','.ave'},  'MEG/EEG: Ricoh (*.sqd;*.con;*.raw;*.ave;*.mrk)', 'RICOH'; ...
                     {'.mat'},               'MEG/EEG: SPM (*.mat/.dat)',            'SPM-DAT'; ...
                     {'.mrk','.sqd','.con','.raw','.ave'},  'MEG/EEG: Yokogawa/KIT (*.sqd;*.con;*.raw;*.ave;*.mrk)', 'KIT'; ...
                     {'.hdf5'},              'MEG/EEG: York Instruments MEGSCAN (.hdf5)', 'MEGSCAN-HDF5'; ...
                     {'.bst'},               'MEG/EEG: Brainstorm binary (*.bst)',   'BST-BIN'; ...
                     {'.adicht'},            'EEG: ADInstruments LabChart (*.adicht)', 'EEG-ADICHT'; ...
                     {'.msr'},               'EEG: ANT ASA (*.msr)',                 'EEG-ANT-MSR'; ...
                     {'.cnt','.avr'},        'EEG: ANT EEProbe (*.cnt;*.avr)',       'EEG-ANT-CNT'; ...
                     {'*'},                  'EEG: ASCII text (*.*)',                'EEG-ASCII'; ...
                     {'.bdf'},               'EEG: BDF (*.bdf)',                     'EEG-BDF'; ...
                     {'.avr','.mux','.mul'}, 'EEG: BESA exports (*.avr;*.mul;*.mux)', 'EEG-BESA'; ...
                     {'.ns1','.ns2','.ns3','.ns4','.ns5','.ns6'}, 'EEG: Blackrock NeuroPort (*.nsX/*.nev)', 'EEG-BLACKROCK';
                     {'.eeg','.dat'},        'EEG: BrainAmp (*.eeg;*.dat)',          'EEG-BRAINAMP'; ...
                     {'.txt'},               'EEG: BrainVision Analyzer (*.txt)',    'EEG-BRAINVISION'; ...
                     {'.sef','.ep','.eph'},  'EEG: Cartool (*.sef;*.ep;*.eph)',      'EEG-CARTOOL'; ...
                     {'.smr','.son'},        'EEG: CED Spike2 old 32bit (*.smr;*.son)',  'EEG-SMR'; ...
                     {'.smr','.smrx'},       'EEG: CED Spike2 new 64bit (*.smr;*.smrx)', 'EEG-SMRX'; ...
                     {'.rda'},               'EEG: Compumedics ProFusion Sleep (*.rda)',  'EEG-COMPUMEDICS-PFS'; ...
                     {'.dat','.cdt'},        'EEG: Curry (*.dat;*.cdt)',             'EEG-CURRY'; ...
                     {'.bin'},               'EEG: Deltamed Coherence-Neurofile (*.bin)', 'EEG-DELTAMED'; ...
                     {'.edf','.rec'},        'EEG: EDF / EDF+ (*.rec;*.edf)',        'EEG-EDF'; ...
                     {'.set'},               'EEG: EEGLAB (*.set)',                  'EEG-EEGLAB'; ...
                     {'.raw'},               'EEG: EGI Netstation RAW (*.raw)',      'EEG-EGI-RAW'; ...
                     {'.mff','.bin'},        'EEG: EGI-Philips (*.mff)',             'EEG-EGI-MFF'; ...
                     {'.edf'},               'EEG: EmotivPRO (*.edf)',               'EEG-EMOTIV'; ...
                     {'.mat','.hdf5'},       'EEG: g.tec Matlab (*.mat,*.hdf5)',     'EEG-GTEC'; ...
                     {'.rhd','.rhs'},        'EEG: Intan (*.rhd,*.rhs)',             'EEG-INTAN'; ...
                     {'.mb2'},               'EEG: MANSCAN (*.mb2)',                 'EEG-MANSCAN'; ...
                     {'.mat'},               'EEG: Matlab matrix (*.mat)',           'EEG-MAT'; ...
                     {'.csv'},               'EEG: Muse (*.csv)',                    'EEG-MUSE-CSV'; ...
                     {'.trc'},               'EEG: Micromed (*.trc)',                'EEG-MICROMED'; ...
                     {'.ncs'},               'EEG: Neuralynx (*.ncs)',               'EEG-NEURALYNX'; ...
                     {'.nwb'},               'EEG: Neurodata Without Borders (*.nwb)','NWB'; ...
                     {'.bin'},               'EEG: NeurOne session folder',          'EEG-NEURONE'; ...
                     {'.cnt','.avg','.eeg','.dat'}, 'EEG: Neuroscan (*.cnt;*.eeg;*.avg;*.dat)', 'EEG-NEUROSCAN'; ...
                     {'.eeg','.dat'},        'EEG: NeuroScope (*.eeg;*.dat)',        'EEG-NEUROSCOPE'; ...
                     {'.e'},                 'EEG: Nicolet (*.e)',                   'EEG-NICOLET'; ...
                     {'.eeg'},               'EEG: Nihon Kohden (*.eeg)',            'EEG-NK'; ...
                     {'.dat'},               'EEG: Open Ephys flat binary (*.dat)',  'EEG-OEBIN'; ...
                     {'.plx','.pl2'},        'EEG: Plexon (*.plx;.pl2)'              'EEG-PLEXON'; ...
                     {'.ns1','.ns2','.ns3','.ns4','.ns5','.ns6'}, 'EEG: Ripple Trellis (*.nsX/*.nev)', 'EEG-RIPPLE'; ...
                     {'.h5'},                'EEG: The Virtual Brain (*_TimeSeriesEEG.h5)', 'EEG-TVB'; ...
                     {'.tbk'},               'EEG: Tucker Davis Technologies (*.tbk)',    'EEG-TDT'; ...
                     {'.csv'},               'EEG: Wearable Sensing (*.csv)',        'EEG-WS-CSV'; ...
                     {'.trc','.eeg','.e','.bin','.rda','.edf','.bdf'}, 'SEEG: Deltamed/Micromed/NK/Nicolet/BrainAmp/EDF', 'SEEG-ALL'; ...
                     {'.trc','.eeg','.e','.bin','.rda','.edf','.bdf'}, 'ECOG: Deltamed/Micromed/NK/Nicolet/BrainAmp/EDF', 'ECOG-ALL'; ...
                     {'.nirs'},              'NIRS: Brainsight (*.nirs)',            'NIRS-BRS'; ...
                     {'.bnirs','.jnirs','.snirf'}, 'NIRS: SNIRF (*.snirf)',          'NIRS-SNIRF'; ...
                     {'.edf'},               'EyeLink eye tracker (*.edf)',          'EYELINK'; ...
                    };

            case 'dataout'
                argout1 = {...
                    {'.bst'},   'MEG/EEG: Brainstorm binary (*.bst)',          'BST-BIN'; ...
                    {'.mat'},   'MEG/EEG: FieldTrip timelock (*.mat)',         'FT-TIMELOCK'; ...
                    {'.mat'},   'MEG/EEG: SPM (*.mat/.dat)',                   'SPM-DAT'; ...
                    {'.eeg'},   'EEG: BrainVision BrainAmp (*.eeg)',           'EEG-BRAINAMP'; ...
                    {'.eph'},   'EEG: Cartool EPH (*.eph)',                    'EEG-CARTOOL-EPH'; ...
                    {'.raw'},   'EEG: EGI NetStation RAW (*.raw)',             'EEG-EGI-RAW'; ...
                    {'.edf'},   'EEG: European Data Format (*.edf)',           'EEG-EDF'; ...
                    {'.snirf'}, 'NIRS: SNIRF (*.snirf)',                       'NIRS-SNIRF'; ...
                    {'.txt'},   'ASCII: Space-separated, fixed column size (*.txt)', 'ASCII-SPC'; ...
                    {'.txt'},   'ASCII: Space-separated with header, fixed column size (*.txt)', 'ASCII-SPC-HDR'; ...
                    {'.tsv'},   'ASCII: Tab-separated (*.tsv)',                'ASCII-TSV'; ...
                    {'.tsv'},   'ASCII: Tab-separated with header (*.tsv)',    'ASCII-TSV-HDR'; ...
                    {'.tsv'},   'ASCII: Tab-separated with header transposed (*.tsv)',   'ASCII-TSV-HDR-TR'; ...
                    {'.csv'},   'ASCII: Comma-separated (*.csv)',              'ASCII-CSV'; ...
                    {'.csv'},   'ASCII: Comma-separated with header (*.csv)',  'ASCII-CSV-HDR'; ...
                    {'.csv'},   'ASCII: Comma-separated with header transposed (*.csv)', 'ASCII-CSV-HDR-TR'; ...
                    {'.xlsx'},  'Microsoft Excel (*.xlsx)',                    'EXCEL'; ...
                    {'.xlsx'},  'Microsoft Excel transposed (*.xlsx)',         'EXCEL-TR'; ...
                    {'_timeseries'}, 'Brainstorm matrix (*timeseries*.mat)',   'BST'; ...
                   };
            case 'rawout'
                argout1 = {...
                    {'.bst'},   'MEG/EEG: Brainstorm binary (*.bst)',  'BST-BIN'; ...
                    {'.mat'},   'MEG/EEG: SPM (*.mat/.dat)',           'SPM-DAT'; ...
                    {'.eeg'},   'EEG: BrainVision BrainAmp (*.eeg)',   'EEG-BRAINAMP'; ...
                    {'.raw'},   'EEG: EGI NetStation RAW (*.raw)',     'EEG-EGI-RAW'; ...
                    {'.edf'},   'EEG: European Data Format (*.edf)',   'EEG-EDF'; ...
                    {'.snirf'}, 'NIRS: SNIRF (*.snirf)',               'NIRS-SNIRF'; ...
                   };
            case 'events'
                argout1 = {...
                    {'.trg'},          'ANT EEProbe (*.trg)',           'ANT'; ...
                    {'.mrk'},          'AnyWave (*.mrk)',               'ANYWAVE'; ...
                    {'.evt'},          'BESA (*.evt)',                  'BESA'; ...
                    {'.tsv'},          'BIDS events: onset, duration, trial_type, channel (*.tsv)', 'BIDS'; ...
                    {'.vmrk'},         'BrainVision BrainAmp (*.vmrk)', 'BRAINAMP'; ...
                    {'_events'},       'Brainstorm (events*.mat)',      'BST'; ...
                    {'.mrk'},          'Cartool (*.mrk)',               'CARTOOL'; ...
                    {'.mrk'},          'CTF MarkerFile (*.mrk)',        'CTF'; ...
                    {'.cef'},          'Curry (*.cef)',                 'CURRY'; ...
                    {'.eve','.fif'},   'Elekta-Neuromag MNE (*.eve;*.fif)',    'FIF'; ...
                    {'.evl','.txt'},   'Elekta-Neuromag Graph (*.evl;*.txt)',  'GRAPH'; ...
                    {'.txt','.mat'},   'FieldTrip trial definition (*.txt;*.mat)', 'TRL'; ...
                    {'.trg'},          'KRISS MEG (*.trg)',             'KDF'; ...
                    {'.ev2'},          'Neuroscan (*.ev2)',             'NEUROSCAN'; ...
                    {'.txt'},          'Nicolet export (*.txt)',        'NICOLET'; ...
                    {'timestamps.npy'},'Open Ephys (timestamps.npy)', 'OEBIN'; ...
                    {'.log'},          'Presentation (*.log)',          'PRESENTATION'; ...
                    {'.mrk','.sqd','.con','.raw','.ave'},   'Ricoh (*.mrk;*.sqd;*.con;*.raw;*.ave)', 'RICOH'; ...
                    {'.txt'},          'XLTEK export (*.txt)',          'XLTEK'; ...
                    {'.mrk','.sqd','.con','.raw','.ave'},   'Yokogawa/KIT (*.mrk;*.sqd;*.con;*.raw;*.ave)', 'KIT'; ...
                    {'.*'},            'Array of times (*.mat;*.*)',    'ARRAY-TIMES'; ...
                    {'.*'},            'Array of samples (*.mat;*.*)',  'ARRAY-SAMPLES'; ...
                    {'.txt','.csv'},   'CSV text file: label, time, duration (*.txt;*.csv)', 'CSV-TIME'; ...
                    {'.*'},            'CTF Video Times (.txt)',        'CTFVIDEO'; ...
                    };
            case 'channel'
                argout1 = {...
                    {'.*'},                        'MEG/EEG: 4D-Neuroimaging/BTi (*.*)',  '4D'; ...
                    {'.meg4','.res4'},             'MEG/EEG: CTF (*.ds;*.meg4;*.res4)',   'CTF' ; ...
                    {'.fif'},                      'MEG/EEG: Elekta-Neuromag (*.fif)',    'FIF'; ...
                    {'.kdf'},                      'MEG/EEG: KRISS MEG (*.kdf)',          'KDF'; ...
                    {'.raw'},                      'MEG/EEG: ITAB (*.raw)',               'ITAB'; ...
                    {'.mrk','.sqd','.con','.raw','.ave'},  'MEG/EEG: Ricoh (*.sqd;*.con;*.raw;*.ave;*.mrk)', 'RICOH'; ...
                    {'.mrk','.sqd','.con','.raw','.ave'},  'MEG/EEG: Yokogawa/KIT (*.sqd;*.con;*.raw;*.ave;*.mrk)', 'KIT'; ...
                    {'.hdf5'},                     'MEG/EEG: York Instruments MEGSCAN (.hdf5)', 'MEGSCAN-HDF5'; ...
                    {'.bst'},                      'MEG/EEG: Brainstorm binary (*.bst)',   'BST-BIN'; ...
                    {'_channel'},                  'MEG/EEG: Brainstorm (channel*.mat)',  'BST'; ...
                    {'.elc'},                      'EEG: ANT ASA/Xensor (*.elc)',         'XENSOR'; ...
                    {'.sfp','.elp','.ela','.eps'}, 'EEG: BESA (*.sfp;*.elp;*.eps/*.ela)', 'BESA'; ...
                    {'.bvef','.bvct','.txt'},      'EEG: BrainVision electrode file (*.bvef,*.bvct,*.txt)', 'BRAINVISION'; ...
                    {'.tsv'},                      'EEG: BIDS electrodes.tsv, subject space mm (*.tsv)',    'BIDS-ORIG-MM'; ...
                    {'.tsv'},                      'EEG: BIDS electrodes.tsv, MNI space mm (*.tsv)',        'BIDS-MNI-MM'; ...
                    {'.els','.xyz'},               'EEG: Cartool (*.els;*.xyz)',          'CARTOOL'; ...
                    {'.eeg'},                      'EEG: MegDraw (*.eeg)',                'MEGDRAW'; ...
                    {'.res','.rs3','.pom'},        'EEG: Curry (*.res;*.rs3;*.pom)',      'CURRY'; ...
                    {'.ced','.xyz','.set'},        'EEG: EEGLAB (*.ced;*.xyz;*.set)',     'EEGLAB'; ...
                    {'.elc'},                      'EEG: EETrak (*.elc)',                 'EETRAK'; ...
                    {'.sfp'},                      'EEG: EGI (*.sfp)',                    'EGI'; ...
                    {'coordinates.xml'},           'EEG: EGI-Philips (coordinates.xml)',  'MFF'; ...
                    {'.elp'},                      'EEG: EMSE (*.elp)',                   'EMSE'; ...
                    {'.pts','.csv'},               'EEG: IntrAnat, subject space (*.pts;*.csv)', 'INTRANAT'; ...
                    {'.pts','.csv'},               'EEG: IntrAnat, MNI space (*.pts;*.csv)',     'INTRANAT_MNI'; ...
                    {'.csv'},                      'EEG: Localite (*.csv)',                      'LOCALITE'; ...
                    {'.dat','.tri','.txt','.asc'}, 'EEG: Neuroscan (*.dat;*.tri;*.txt;*.asc)',   'NEUROSCAN'; ...
                    {'.pos','.pol','.elp','.txt'}, 'EEG: Polhemus (*.pos;*.pol;*.elp;*.txt)',    'POLHEMUS'; ...
                    {'.csv'},                      'EEG: SimNIBS (*.csv)',             'SIMNIBS'; ...
                    {'.h5'},                       'EEG: The Virtual Brain (*_SensorsEEG.h5)',    'TVB'; ...
                    {'*'},                         'EEG: ASCII: Name,XYZ (*.*)',       'ASCII_NXYZ'; ...
                    {'*'},                         'EEG: ASCII: Name,XYZ_MNI (*.*)',   'ASCII_NXYZ_MNI'; ...
                    {'*'},                         'EEG: ASCII: Name,XYZ_World (*.*)', 'ASCII_NXYZ_WORLD'; ...
                    {'*'},                         'EEG: ASCII: Name,XY (*.*)',        'ASCII_NXY'; ...
                    {'*'},                         'EEG: ASCII: XYZ (*.*)',            'ASCII_XYZ'; ...
                    {'*'},                         'EEG: ASCII: XYZ_MNI (*.*)',        'ASCII_XYZ_MNI'; ...
                    {'*'},                         'EEG: ASCII: XYZ_World (*.*)',      'ASCII_XYZ_WORLD'; ...
                    {'*'},                         'EEG: ASCII: XY (*.*)',             'ASCII_XY'; ...
                    {'*'},                         'EEG: ASCII: XYZ,Name (*.*)',       'ASCII_XYZN'; ...
                    {'*'},                         'EEG: ASCII: XYZ_MNI,Name (*.*)',   'ASCII_XYZN_MNI'; ...
                    {'*'},                         'EEG: ASCII: XYZ_World,Name (*.*)', 'ASCII_XYZN_WORLD'; ...
                    {'*'},                         'EEG: ASCII: Name,Theta,Phi (*.*)', 'ASCII_NTP'; ...
                    {'*'},                         'EEG: ASCII: Theta,Phi (*.*)',      'ASCII_TP'; ...
                    };
            case 'channelout'
                argout1 = {...
                    {'.pos'}, 'EEG+Headshape: Polhemus (*.pos)',     'POLHEMUS'; ...
                    {'.eeg'}, 'Headshape: MegDraw (*.eeg)',          'MEGDRAW'; ...
                    {'.pos'}, 'Headshape: Polhemus (*.pos)',         'POLHEMUS-HS'; ...
                    {'.txt'}, 'Headshape: ASCII: XYZ (*.txt)',       'ASCII_XYZ-HS'; ...
                    {'.txt'}, 'Headshape: ASCII: XYZ_World (*.txt)', 'ASCII_XYZ_WORLD-HS'; ...
                    {'.txt'}, 'Headshape: ASCII: Name,XYZ (*.txt)',  'ASCII_NXYZ-HS'; ...
                    {'.txt'}, 'Headshape: ASCII: Name,XYZ_World (*.txt)',  'ASCII_NXYZ_WORLD-HS'; ...
                    {'.txt'}, 'Headshape: ASCII: XYZ,Name (*.txt)',  'ASCII_XYZN-HS'; ...
                    {'.txt'}, 'Headshape: ASCII: XYZ_World,Name (*.txt)',  'ASCII_XYZN_WORLD-HS'; ...
                    {'.sfp'}, 'EEG: BESA (*.sfp)',                   'BESA-SFP'; ...
                    {'.elp'}, 'EEG: BESA (*.elp)',                   'BESA-ELP'; ...
                    {'.xyz'}, 'EEG: Cartool (*.xyz)',                'CARTOOL-XYZ'; ...
                    {'.res'}, 'EEG: Curry (*.res)',                  'CURRY-RES'; ...
                    {'.xyz'}, 'EEG: EEGLAB (*.xyz)',                 'EEGLAB-XYZ'; ...
                    {'.sfp'}, 'EEG: EGI (*.sfp)',                    'EGI'; ...
                    {'.txt'}, 'EEG: ASCII: XYZ (*.txt)',             'ASCII_XYZ-EEG'; ...
                    {'.txt'}, 'EEG: ASCII: XYZ_MNI (*.*)',           'ASCII_XYZ_MNI-EEG'; ...
                    {'.txt'}, 'EEG: ASCII: XYZ_World (*.*)',         'ASCII_XYZ_WORLD-EEG'; ...
                    {'.txt'}, 'EEG: ASCII: Name,XYZ (*.txt)',        'ASCII_NXYZ-EEG'; ...
                    {'.txt'}, 'EEG: ASCII: Name,XYZ_MNI (*.*)',      'ASCII_NXYZ_MNI-EEG'; ...
                    {'.txt'}, 'EEG: ASCII: Name,XYZ_World (*.*)',    'ASCII_NXYZ_WORLD-EEG'; ...
                    {'.txt'}, 'EEG: ASCII: XYZ,Name (*.txt)',        'ASCII_XYZN-EEG'; ...
                    {'.txt'}, 'EEG: ASCII: XYZ_MNI,Name (*.*)',      'ASCII_XYZN_MNI-EEG'; ...
                    {'.txt'}, 'EEG: ASCII: XYZ_World,Name (*.*)',    'ASCII_XYZN_WORLD-EEG'; ...
                    {'.txt'}, 'NIRS: Brainsight (*.txt)',            'BRAINSIGHT-TXT'; ...
                    };
            case 'labelin'
                argout1 = {...
                    {'.dfs'},    'BrainSuite atlas (*.dfs)',      'DFS'; ...
                    {'.annot'},  'FreeSurfer atlas (*.annot)',    'FS-ANNOT'; ...
                    {'.label'},  'FreeSurfer ROI, single scout (*.label)',    'FS-LABEL-SINGLE'; ...
                    {'.label'},  'FreeSurfer ROI, probability map (*.label)', 'FS-LABEL'; ...
                    {'.gii'},    'GIfTI texture (*.gii)',         'GII-TEX'; ...
                    {'.dset'},   'SUMA atlas (*.dset)',           'DSET'; ...
                    {'_scout'},  'Brainstorm scouts (*scout*.mat)', 'BST'; ...
                    {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'Volume mask or atlas (dilated, subject space)', 'MRI-MASK'; ...
                    {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz'},                  'Volume mask or atlas (dilated, MNI space)',     'MRI-MASK-MNI'; ...
                    {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'Volume mask or atlas (no overlap, subject space)', 'MRI-MASK-NOOVERLAP'; ...
                    {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz'},                  'Volume mask or atlas (no overlap, MNI space)',     'MRI-MASK-NOOVERLAP-MNI'; ...
                    };
            case 'resultsout'
                argout1 = {...
                    {'_sources'}, 'Brainstorm sources (*sources*.mat)',        'BST'; ...
                    {'.mat'},   'FieldTrip sources (*.mat)',                   'FT-SOURCES'; ...
                    {'.txt'},   'ASCII: Space-separated, fixed columns size (*.txt)', 'ASCII-SPC'; ...
                    {'.txt'},   'ASCII: Space-separated with header, fixed column size (*.txt)', 'ASCII-SPC-HDR'; ...
                    {'.tsv'},   'ASCII: Tab-separated (*.tsv)',                'ASCII-TSV'; ...
                    {'.tsv'},   'ASCII: Tab-separated with header (*.tsv)',    'ASCII-TSV-HDR'; ...
                    {'.tsv'},   'ASCII: Tab-separated with header transposed (*.tsv)',   'ASCII-TSV-HDR-TR'; ...
                    {'.csv'},   'ASCII: Comma-separated (*.csv)',              'ASCII-CSV'; ...
                    {'.csv'},   'ASCII: Comma-separated with header (*.csv)',  'ASCII-CSV-HDR'; ...
                    {'.csv'},   'ASCII: Comma-separated with header transposed (*.csv)', 'ASCII-CSV-HDR-TR'; ...
                    {'.xlsx'},  'Microsoft Excel (*.xlsx)',                    'EXCEL'; ...
                    {'.xlsx'},  'Microsoft Excel transposed (*.xlsx)',         'EXCEL-TR'; ...
                    };
            case 'timefreqout'
                argout1 = {...
                    {'_timefreq'}, 'Brainstorm structure (*timefreq*.mat)',    'BST'; ...
                    {'.mat'},   'FieldTrip freq (*.mat)',                      'FT-FREQ'; ...
                    {'.txt'},   'ASCII: Space-separated, fixed columns size (*.txt)', 'ASCII-SPC'; ...
                    {'.txt'},   'ASCII: Space-separated with header, fixed column size (*.txt)', 'ASCII-SPC-HDR'; ...
                    {'.tsv'},   'ASCII: Tab-separated (*.tsv)',                'ASCII-TSV'; ...
                    {'.tsv'},   'ASCII: Tab-separated with header (*.tsv)',    'ASCII-TSV-HDR'; ...
                    {'.tsv'},   'ASCII: Tab-separated with header transposed (*.tsv)',   'ASCII-TSV-HDR-TR'; ...
                    {'.csv'},   'ASCII: Comma-separated (*.csv)',              'ASCII-CSV'; ...
                    {'.csv'},   'ASCII: Comma-separated with header (*.csv)',  'ASCII-CSV-HDR'; ...
                    {'.csv'},   'ASCII: Comma-separated with header transposed (*.csv)', 'ASCII-CSV-HDR-TR'; ...
                    {'.xlsx'},  'Microsoft Excel (*.xlsx)',                    'EXCEL'; ...
                    {'.xlsx'},  'Microsoft Excel transposed (*.xlsx)',         'EXCEL-TR'; ...
                    };
            case 'matrixout'
                argout1 = {...
                    {'_matrix'}, 'Brainstorm structure (*matrix*.mat)',        'BST'; ...
                    {'.mat'},   'FieldTrip timelock (*.mat)',                  'FT-TIMELOCK'; ...
                    {'.txt'},   'ASCII: Space-separated, fixed columns size (*.txt)', 'ASCII-SPC'; ...
                    {'.txt'},   'ASCII: Space-separated with header, fixed column size (*.txt)', 'ASCII-SPC-HDR'; ...
                    {'.tsv'},   'ASCII: Tab-separated (*.tsv)',                'ASCII-TSV'; ...
                    {'.tsv'},   'ASCII: Tab-separated with header (*.tsv)',    'ASCII-TSV-HDR'; ...
                    {'.tsv'},   'ASCII: Tab-separated with header transposed (*.tsv)',   'ASCII-TSV-HDR-TR'; ...
                    {'.csv'},   'ASCII: Comma-separated (*.csv)',              'ASCII-CSV'; ...
                    {'.csv'},   'ASCII: Comma-separated with header (*.csv)',  'ASCII-CSV-HDR'; ...
                    {'.csv'},   'ASCII: Comma-separated with header transposed (*.csv)', 'ASCII-CSV-HDR-TR'; ...
                    {'.xlsx'},  'Microsoft Excel (*.xlsx)',                    'EXCEL'; ...
                    {'.xlsx'},  'Microsoft Excel transposed (*.xlsx)',         'EXCEL-TR'; ...
                    };
            case 'montagein'
                argout1 = {...
                    {'.sel'},     'MNE selection files (*.sel)',              'MNE'; ...
                    {'.mon'},     'Text montage files (*.mon)',               'MON'; ...
                    {'_montage'}, 'Brainstorm montage files (montage_*.mat)', 'BST';
                    {'.csv'},     'Comma-separated montage files (*.csv)',    'CSV'; ...
                    {'.xml'},     'Compumedics ProFusion montages (*.xml)',   'EEG-COMPUMEDICS-PFS'};
            case 'montageout'
                argout1 = {...
                    {'.sel'},     'MNE selection files (*.sel)',              'MNE'; ...
                    {'.mon'},     'Text montage files (*.mon)',               'MON'; ...
                    {'_montage'}, 'Brainstorm montage files (montage_*.mat)', 'BST'};
            case 'fibers'
                argout1 = {...
                    {'.trk'},    'TrackVis (*.trk)',                       'TRK'; ...
                    {'_fibers'}, 'Brainstorm fibers files (fibers_*.mat)', 'BST'};
        end
        

%% ===== FONTS =====
    case 'FigFont'
        if ispc
            argout1 = 8;
        else
            argout1 = 9;
        end
        InterfaceScaling = bst_get('InterfaceScaling');
        if (InterfaceScaling ~= 100)
            argout1 = argout1 * InterfaceScaling / 100;
        end
        
    case 'Font'
        % Default font size
        if (nargin < 2)
            if strncmp(computer,'MAC',3)
                fontSize = 12;
            else
                fontSize = 11;
            end
        % Font size in input
        else
            fontSize = varargin{2};
        end
        % Adjust for interface scaling
        fontSize = fontSize * bst_get('InterfaceScaling') / 100;
        
        % Font types
        fontTypes = {};
        if (nargin >= 3)
            fontTypes{end + 1} = varargin{3};
        end
        fontTypes{end + 1} = 'Arial';  % Default font
        fontTypes{end + 1} = 'Liberation Sans';  % Free Arial substitute
        
        % Check for cached font
        foundFont = 0;
        for iFont = 1 : length(fontTypes)
            strCache = strrep(sprintf('%s%d', fontTypes{iFont}, round(fontSize*100)), ' ', '_');
            if ~isempty(GlobalData) && isfield(GlobalData, 'Program') && isfield(GlobalData.Program, 'FontCache') && isfield(GlobalData.Program.FontCache, strCache)
                argout1 = GlobalData.Program.FontCache.(strCache);
                foundFont = 1;
                break;
            end
        end
            
        % If font not cached, find first supported font
        if ~foundFont
            ge = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment();
            allFonts = cell(ge.getAvailableFontFamilyNames());
            
            for iFont = 1 : length(fontTypes)
                if any(strcmp(fontTypes{iFont}, allFonts))
                    fontType = fontTypes{iFont};
                    foundFont = 1;
                    break;
                end
            end
            
            if ~foundFont
                fontType = 'SansSerif';  % If nothing else works.
            end
            
            strCache = strrep(sprintf('%s%d', fontType, round(fontSize*100)), ' ', '_');
            argout1 = java.awt.Font(fontType, java.awt.Font.PLAIN, fontSize);
            GlobalData.Program.FontCache.(strCache) = argout1;
        end
        
%% ==== PANEL CONTAINERS ====
    case 'PanelContainer'    
        % Get Brainstorm GUI context structure
        bst_GUI = GlobalData.Program.GUI;
        if (isempty(bst_GUI) || ~isfield(bst_GUI, 'panelContainers'))
            error('Brainstorm GUI is not yet initialized');
        end
        
        % Get ContainerName in argument
        if ((nargin >= 2) && (ischar(varargin{2})))
            ContainerName = varargin{2};
        % If no container name in argument : just display all the container names
        else
            disp('Registered panel containers :');
            for iContainer = 1:length(bst_GUI.panelContainers)
                disp(['    - ' bst_GUI.panelContainers(iContainer).name]);
            end
            return
        end

        % Look for containerName in all the registered panel containers
        iContainer = 1;
        found = 0;
        while (~found (iContainer <= length(bst_GUI.panelContainers)))
             if (strcmpi(ContainerName, bst_GUI.panelContainers(iContainer).name))
                 found = 1;
             else
                 iContainer = iContainer + 1;
             end
        end
        % If container is found : return it
        if (found)
            argout1 = bst_GUI.panelContainers(iContainer).jHandle;
        else
            % warning('Brainstorm:InvalidContainer', 'Container ''%s'' could not be found.', ContainerName);
        end

        
%% ==== PANELS ====
    case 'Panel'    
        % Get Brainstorm GUI context structure
        if (isempty(GlobalData) || isempty(GlobalData.Program.GUI) || ~isfield(GlobalData.Program.GUI, 'panels'))
            return
        end
        listPanels = GlobalData.Program.GUI.panels;
        % Get Panel in argument
        if ((nargin >= 2) && (ischar(varargin{2})))
            PanelName = varargin{2};
        % If no panel name in argument : just display all the panels names
        else
            disp('Registered panels :');
            for iContainer = 1:length(listPanels)
                disp(['    - ' get(listPanels(iContainer), 'name')]);
            end
            return
        end
        % Look for panelName in all the registered panels
        iPanel = find(strcmpi(PanelName, get(listPanels, 'name')), 1);
        if ~isempty(iPanel)
            argout1 = listPanels(iPanel);
            argout2   = iPanel;
        end
                
        
%% ==== PANEL CONTROLS ====
%  Calls : bst_get('PanelControls', PanelName)
    case 'PanelControls'
        % Get Panel name in argument
        if ((nargin >= 2) && (ischar(varargin{2})))
            PanelName = varargin{2};
        else
            error('Invalid call to bst_get()');
        end
        % Find BstPanel with this name
        bstPanel = bst_get('Panel', PanelName);
        % If panel was found : return its controls
        if ~isempty(bstPanel)
            argout1 = get(bstPanel, 'sControls');
        end
        
%% ===== NODES COPY =====
%  Calls : bst_get('Clipboard')
    case 'Clipboard'
        argout1 = GlobalData.Program.Clipboard.Nodes;
        argout2 = GlobalData.Program.Clipboard.isCut;
        
%% ==== DIRECTORIES ====
    case 'DirDefaultSubject'
        argout1 = '@default_subject';
    case 'DirDefaultStudy'
        argout1 = '@default_study';
    case 'DirAnalysisIntra'
        argout1 = '@intra';
    case 'DirAnalysisInter'
        argout1 = '@inter';
    case 'NormalizedSubjectName'
        argout1 = 'Group_analysis';
        
%% ==== OTHER ====
    case 'ResizeFunction'
        if (bst_get('MatlabVersion') <= 803)
            argout1 = 'ResizeFcn';
        else
            argout1 = 'SizeChangedFcn';
        end
    case 'groot'
        if (bst_get('MatlabVersion') <= 803)
            argout1 = 0;
        else
            argout1 = groot;
        end
    case 'JFrame'
        hFig = varargin{2};
        MatlabVersion = bst_get('MatlabVersion');
        jFrame = [];
        try
            if (MatlabVersion <= 705)
                jf = get(hFig, 'javaframe');
                jFrame = jf.fFigureClient.getWindow();
            elseif (MatlabVersion <= 712)
                jf = get(handle(hFig), 'javaframe');
                jFrame = jf.fFigureClient.getWindow();
            elseif (MatlabVersion <= 803)
                jf = get(handle(hFig), 'javaframe');
                jFrame = jf.fHG1Client.getWindow();
            elseif (MatlabVersion < 907)    % Matlab >= 2019b deprecated the JavaFrame property
                warning('off', 'MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
                jf = get(hFig, 'javaframe');
                warning('on', 'MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
                jFrame = jf.fHG2Client.getWindow();
            else
                disp('BST> Error: Matlab 2019b deprecated the JavaFrame property.');
            end
        catch
            disp('BST> Warning: Cannot get the JavaFrame property for the selected figure.');
        end
        argout1 = jFrame;
        
%% ==== ERROR ====
    otherwise
        error(sprintf('Invalid context : "%s"', contextName));
end
end




%% ==== HELPERS ====
% Return all the protocol studies that have a given file in its structures
% Possible field names: Result.DataFile, Result.FileName, Data.FileName, Channel.FileName
%
% USAGE:  [sFoundStudy, iFoundStudy, iItem] = findFileInStudies(fieldGroup, fieldName, fieldFile, iStudiesList)
%         [sFoundStudy, iFoundStudy, iItem] = findFileInStudies(fieldGroup, fieldName, fieldFile)
function [sFoundStudy, iFoundStudy, iItem] = findFileInStudies(fieldGroup, fieldName, fieldFile, iStudiesList)
    global GlobalData;
    sFoundStudy = [];
    iFoundStudy = [];
    iItem       = [];
    % If no file provided, return
    if isempty(fieldFile)
        return;
    end
    % Extract folder(s) of the file(s) we're looking for
    fieldParts = strfind(fieldFile, '|');
    if ~isempty(fieldParts)
        fieldParts(end+1) = length(fieldFile);
        fieldFolders = {};
        iLast = 1;
        for iPart = 1:length(fieldParts)
            folder = fileparts(fieldFile(iLast:fieldParts(iPart)-1));
            if ~isempty(folder)
                fieldFolders{end + 1} = folder;
            end
            iLast = fieldParts(iPart) + 1;
        end
    else
        fieldFolders = {fileparts(fieldFile)};
    end
    % Get protocol information
    ProtocolStudies = GlobalData.DataBase.ProtocolStudies(GlobalData.DataBase.iProtocol);
    % List studies to process
    if (nargin < 4) || isempty(iStudiesList)
        iStudiesList = [-2, -3, 1:length(ProtocolStudies.Study)];
    end
    
    % NORMAL STUDIES: Look for surface file in all the surfaces of all subjects
    for iStudy = iStudiesList
        % Get study
        switch (iStudy)
            case -2,    sStudy = ProtocolStudies.AnalysisStudy;
            case -3,    sStudy = ProtocolStudies.DefaultStudy;
            otherwise,  sStudy = ProtocolStudies.Study(iStudy);
        end
        % Check if field is available for the study
        if isempty(sStudy.(fieldGroup))
            continue;
        end
         % Check we are in the correct folder
        if ~any(file_compare(fieldFolders, fileparts(sStudy.FileName)))
            continue;
        end
        % Get list of files from study
        filesList = {sStudy.(fieldGroup).(fieldName)};
        if isempty(filesList)
            continue;
        end
        % Replace empty cells with empty strings
        iValidFiles = find(cellfun(@ischar, filesList));
        if isempty(iValidFiles)
            continue;
        end
        % Find target in this list
        iItem = find(file_compare(filesList(iValidFiles), fieldFile));
        if ~isempty(iItem)
            sFoundStudy  = sStudy;
            iFoundStudy  = iStudy;
            iItem = iValidFiles(iItem);
            return
        end
    end
end


%% ===== FILL MISSING FIELDS =====
function bstPref = FillMissingFields(PrefName, defPref)
    global GlobalData;
    if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, PrefName)
        bstPref = GlobalData.Preferences.(PrefName);
        bstPref = struct_copy_fields(bstPref, defPref, 0);
    else
        bstPref = defPref;
    end
end








To change parameters or database structures: bst_set.m.

function bst_set( varargin )
% BST_SET: Set a Brainstorm structure.
%
% DESCRIPTION:  This function is used to abstract the way that these structures are stored.
%
% USAGE:
% ====== DIRECTORIES ==================================================================
%    - bst_set('BrainstormHomeDir', BrainstormHomeDir)
%    - bst_set('BrainstormTmpDir',  BrainstormTmpDir)
%    - bst_set('BrainstormDbDir',   BrainstormDbDir)
%    - bst_set('LastUsedDirs',      sDirectories)
%    - bst_set('BrainSuiteDir',     BrainSuiteDir)
%    - bst_set('PythonExe',         PythonExe)
%    - bst_set('PluginCustomPath',  PluginCustomPath)
%
% ====== PROTOCOLS ====================================================================
%    - bst_set('iProtocol',         iProtocol)
%    - bst_set('ProtocolInfo',      sProtocolInfo)
%    - bst_set('ProtocolSubjects',  ProtocolSubjects)
%    - bst_set('isProtocolLoaded',  isProtocolLoaded)
%    - bst_set('isProtocolModified',isProtocolModified)
%    - bst_set('ProtocolStudies',   ProtocolStudies)
%    - bst_set('Study',   iStudy,   sStudy)    : Set a study in current protocol 
%    - bst_set('Subject', iSubject, sSubject)  : Set a subject in current protocol
%
% ====== GUI =================================================================
%    - bst_set('Layout',    sLayout)
%    - bst_set('Layout',    PropName, PropValue)
%    - bst_set('Clipboard', Nodes, isCut)  : Copy operation from the tree
%
% ====== CONFIGURATION =================================================================
%    - bst_set('Version',      Version)
%    - bst_set('ByteOrder',    value)        : 'b' for big endian, 'l' for little endian
%    - bst_set('AutoUpdates',  isAutoUpdates)
%    - bst_set('ExpertMode',   isExpertMode)
%    - bst_set('DisplayGFP',   isDisplayGFP)
%    - bst_set('DownsampleTimeSeries',  isDownsampleTimeSeries)
%    - bst_set('GraphicsSmoothing',     isGraphicsSmoothing)
%    - bst_set('ForceMatCompression',   isForceCompression)
%    - bst_set('IgnoreMemoryWarnings',  isIgnoreMemoryWarnings)
%    - bst_set('SystemCopy',            isSystemCopy)
%    - bst_set('DisableOpenGL',         isDisableOpenGL)
%    - bst_set('InterfaceScaling',      InterfaceScaling)
%    - bst_set('TSDisplayMode',         TSDisplayMode)    : {'butterfly','column'}
%    - bst_set('ElectrodeConfig',       ElectrodeConfig, Modality)
%    - bst_set('DefaultFormats'         defaultFormats)
%    - bst_set('BFSProperties',         [scalpCond,skullCond,brainCond,scalpThick,skullThick])
%    - bst_set('ImportEegRawOptions',   ImportEegRawOptions)
%    - bst_set('BugReportOptions',      BugReportOptions)
%    - bst_set('DefaultSurfaceDisplay', displayStruct)
%    - bst_set('MagneticExtrapOptions', extrapStruct)
%    - bst_set('TimefreqOptions_morlet',  Options)
%    - bst_set('TimefreqOptions_fft',     Options)
%    - bst_set('TimefreqOptions_psd',     Options)
%    - bst_set('TimefreqOptions_hilbert', Options)
%    - bst_set('TimefreqOptions_plv',     Options)
%    - bst_set('OpenMEEGOptions',         Options)
%    - bst_set('DuneuroOptions',         Options)
%    - bst_set('GridOptions_headmodel',   Options)
%    - bst_set('GridOptions_dipfit',      Options)
%    - bst_set('UniformizeTimeSeriesScales', isUniform)
%    - bst_set('FlipYAxis',             isFlipY)
%    - bst_set('AutoScaleY',            isAutoScaleY)
%    - bst_set('FixedScaleY',           Modality,  Value)
%    - bst_set('XScale',                XScale)
%    - bst_set('YScale',                YScale)
%    - bst_set('ShowXGrid',             isShowXGrid)
%    - bst_set('ShowYGrid',             isShowYGrid)
%    - bst_set('ShowZeroLines',         isShowZeroLines)
%    - bst_set('ShowEventsMode',        ShowEventsMode)
%    - bst_set('Resolution',            [resX,resY])
%    - bst_set('UseSigProcToolbox',     UseSigProcToolbox)
%    - bst_set('RawViewerOptions',      RawViewerOptions)
%    - bst_set('TopoLayoutOptions',     TopoLayoutOptions)
%    - bst_set('StatThreshOptions',     StatThreshOptions)
%    - bst_set('ContactSheetOptions',   ContactSheetOptions)
%    - bst_set('ProcessOptions',        ProcessOptions)
%    - bst_set('MriOptions',            MriOptions)
%    - bst_set('CustomColormaps',       CustomColormaps)
%    - bst_set('DigitizeOptions',       DigitizeOptions)
%    - bst_set('ReadOnly',              ReadOnly)
%    - bst_set('LastPsdDisplayFunction', LastPsdDisplayFunction)
%    - bst_set('PlotlyCredentials',     Username, ApiKey, Domain)
%    - bst_set('KlustersExecutable',    ExecutablePath)
%    - bst_set('ExportBidsOptions'),    ExportBidsOptions)
%
% SEE ALSO bst_get

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
% 
% Copyright (c)2000-2020 University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
% 
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
%
% For more information type "brainstorm license" at command prompt.
% =============================================================================@
%
% Authors: Francois Tadel, 2008-2021
%          Martin Cousineau, 2017

global GlobalData;

%% ==== PARSE INPUTS ====
if ((nargin >= 1) && ischar(varargin{1}))
    contextName  = varargin{1};
    if (nargin >= 2)
        contextValue = varargin{2};
    else
        contextValue = [];
    end
else
    error('Usage : bst_set(contextName, contextValue)');
end

% Get required context structure
switch contextName      
%% ==== BRAINSTORM CONFIGURATION ====
    case 'Version'
        GlobalData.Program.Version = contextValue;
    case 'BrainstormHomeDir'
        GlobalData.Program.BrainstormHomeDir = contextValue;
    case 'BrainstormDbDir'
        GlobalData.DataBase.BrainstormDbDir = contextValue;
    case 'BrainstormTmpDir'
        GlobalData.Preferences.BrainstormTmpDir = contextValue;

%% ==== PROTOCOL ====
    case 'iProtocol'
        if isnumeric(contextValue)
            GlobalData.DataBase.iProtocol = contextValue;
        else
            error('iProtocol should be a number.');
        end
    case {'ProtocolSubjects', 'ProtocolStudies'}
        for structField = fieldnames(contextValue)'
            GlobalData.DataBase.(contextName)(GlobalData.DataBase.iProtocol).(structField{1}) = contextValue.(structField{1});
        end
        GlobalData.DataBase.isProtocolModified(GlobalData.DataBase.iProtocol) = 1;
    case 'ProtocolInfo'
        for structField = fieldnames(contextValue)'
            GlobalData.DataBase.(contextName)(GlobalData.DataBase.iProtocol).(structField{1}) = contextValue.(structField{1});
        end
    case 'isProtocolLoaded'
        GlobalData.DataBase.isProtocolLoaded(GlobalData.DataBase.iProtocol) = contextValue;
    case 'isProtocolModified'
        GlobalData.DataBase.isProtocolModified(GlobalData.DataBase.iProtocol) = contextValue;

%% ==== SUBJECT ====
    case 'Subject'
        % Get subjects list
        ProtocolSubjects = bst_get('ProtocolSubjects');
        iSubject = varargin{2};
        sSubject = varargin{3};
        % If default subject
        if (iSubject == 0)
            ProtocolSubjects.DefaultSubject = sSubject;
        else
            ProtocolSubjects.Subject(iSubject) = sSubject;
        end
        % Update DataBase
        bst_set('ProtocolSubjects', ProtocolSubjects);
        
        
%% ==== STUDY ====
    case 'Study'
        % Get studies list
        ProtocolStudies = bst_get('ProtocolStudies');
        iStudies = varargin{2};
        sStudies = varargin{3};
        iAnalysisStudy = -2;
        iDefaultStudy  = -3;
        for i = 1:length(iStudies)
            % Normal study
            if (iStudies(i) > 0)
                ProtocolStudies.Study(iStudies(i)) = sStudies(i);
            % Inter-subject analysis study
            elseif (iStudies(i) == iAnalysisStudy)
                ProtocolStudies.AnalysisStudy = sStudies(i);
            % Default study
            elseif (iStudies(i) == iDefaultStudy)
                ProtocolStudies.DefaultStudy = sStudies(i);
            end
        end
        % Update DataBase
        bst_set('ProtocolStudies', ProtocolStudies);
        
        
%% ==== GUI ====
    % USAGE: bst_set('Layout', sLayout)
    %        bst_set('Layout', PropName, PropValue)
    case 'Layout'
        if (nargin == 2) && isstruct(contextValue)
            GlobalData.Preferences.Layout = contextValue;
            isUpdateScreens = 0;
        elseif (nargin == 3) && ischar(contextValue) && isfield(GlobalData.Preferences, 'Layout') && isfield(GlobalData.Preferences.Layout, contextValue)
            GlobalData.Preferences.Layout.(contextValue) = varargin{3};
            isUpdateScreens = strcmpi(contextValue, 'DoubleScreen');
        else
            error('Invalid call to bst_set.');
        end
        % Update screen configuration
        GlobalData.Program.ScreenDef = gui_layout('GetScreenClientArea');
        % Update layout right now
        gui_layout('Update');
        % If the number of screen was changed: update the maximum size of the Brainstorm window
        if isUpdateScreens
            gui_layout('UpdateMaxBstSize');
        end
        
    % USAGE: bst_set('FixedScaleY', [])
    %        bst_set('FixedScaleY', Modality, Value)
    case 'FixedScaleY'
        if (nargin == 3) && ~isempty(contextValue) && ~isempty(varargin{3})
            GlobalData.Preferences.FixedScaleY.(contextValue) = varargin{3};
        elseif (nargin == 2) && isempty(contextValue)
            GlobalData.Preferences.FixedScaleY = struct();
        end
        
    case 'ByteOrder'
        switch(contextValue)
            case {'b','ieee-le','n'}
                GlobalData.Preferences.ByteOrder = 'b';
            case {'l','ieee-be'}
                GlobalData.Preferences.ByteOrder = 'l';
            otherwise
                error('Invalid byte order.');
        end
        
    case 'Clipboard'
        if (length(varargin) >= 3)
            isCut = varargin{3};
        else
            isCut = 0;
        end
        GlobalData.Program.Clipboard.Nodes = contextValue;
        GlobalData.Program.Clipboard.isCut = isCut;
        
    case 'ElectrodeConfig'
        Modality = varargin{2};
        ElectrodeConf = varargin{3};
        if ~ismember(Modality, {'EEG','SEEG','ECOG'})
            error(['Invalid modality: ' Modality]);
        end
        GlobalData.Preferences.(contextName).(Modality) = ElectrodeConf;
        
    case {'UniformizeTimeSeriesScales', 'XScale', 'YScale', 'FlipYAxis', 'AutoScaleY', 'ShowXGrid', 'ShowYGrid', 'ShowZeroLines', 'ShowEventsMode', ...
          'Resolution', 'AutoUpdates', 'ExpertMode', 'DisplayGFP', 'ForceMatCompression', 'GraphicsSmoothing', 'DownsampleTimeSeries', ...
          'DisableOpenGL', 'InterfaceScaling', 'TSDisplayMode', 'UseSigProcToolbox', 'LastUsedDirs', 'DefaultFormats', ...
          'BFSProperties', 'ImportDataOptions', 'ImportEegRawOptions', 'RawViewerOptions', 'MontageOptions', 'TopoLayoutOptions', ...
          'StatThreshOptions', 'ContactSheetOptions', 'ProcessOptions', 'BugReportOptions', 'DefaultSurfaceDisplay', ...
          'MagneticExtrapOptions', 'MriOptions', 'NodelistOptions', 'IgnoreMemoryWarnings', 'SystemCopy', ...
          'TimefreqOptions_morlet', 'TimefreqOptions_hilbert', 'TimefreqOptions_fft', 'TimefreqOptions_psd', 'TimefreqOptions_plv', ...
          'OpenMEEGOptions', 'DuneuroOptions', 'DigitizeOptions', 'CustomColormaps', 'PluginCustomPath', 'BrainSuiteDir', 'PythonExe', ...
          'GridOptions_headmodel', 'GridOptions_dipfit', 'LastPsdDisplayFunction', 'KlustersExecutable', 'ExportBidsOptions'}
        GlobalData.Preferences.(contextName) = contextValue;

    case 'ReadOnly'
        GlobalData.DataBase.isReadOnly = contextValue;
    
    case 'PlotlyCredentials'
        if length(varargin) ~= 4
            error('Invalid call to bst_set.');
        end
        [username, apiKey, domain] = varargin{2:4};
        
        if isempty(domain)
            % Default Plot.ly server
            domain = 'http://plot.ly';
        end
        
        % Plotly needs a URL with HTTP and no trailing slash.
        if strfind(domain, 'https://')
            domain = strrep(domain, 'https://', 'http://');
        elseif isempty(strfind(domain, 'http://'))
            domain = ['http://', domain];
        end
        if domain(end) == '/'
            domain = domain(1:end-1);
        end
        
        saveplotlycredentials(username, apiKey);
        saveplotlyconfig(domain);
        
%% ==== ERROR ====
    otherwise
        error('Invalid context : ''%s''', contextName);
        

end





File structures

The structures of the different types of files were described in the sections "On the hard drive" of the introduction tutorials. Here is a summary of all these sections:

Continuous recordings: File type "raw", Event markers.
Imported recordings: File type "data", Import epochs and Average response.
Power spectrum: File type "timefreq", Power spectrum and frequency filters.
Channel files: File type "channel", Channel file / MEG-MRI coregistration.
SSP/ICA projectors: Saved in the channel files, Artifact cleaning with SSP.
Head models: File type "headmodel", Head model.
Noise covariance: File types "noisecov" and "ndatacov", Noise and data covariance matrices.
Source files: File types "results" and "link", Source estimation.
Time-frequency: File type "timefreq", Time-frequency.
Statistics: File types "pdata", "presults", "ptimefreq" and "pmatrix", Statistics.
MRI volumes: File type "subjectimage", Display the anatomy.
Surfaces: File type "tess", Display the anatomy.
Scouts and atlases: Saved in the surface files, Scouts.

Custom processing

In many situations, you will find useful to read the files available in the database, and maybe modify them. The easiest approaches do not require any scripting, we will start by reviewing them quickly.

Process: Run Matlab command

If you want to modify the values saved in a file (eg. the field "F" from a "data" file), the easiest way is probably to use the process1 File > Run Matlab command. It is also available from Process2 in the category "Other".

It loads the files in input and run them through a piece of Matlab code that you can edit freely. It can extend a lot the flexibility of the Brainstorm pipeline manager, providing an easy access to any Matlab function or script.

The corresponding script looks like this:

sFiles = bst_process('CallProcess', 'process_matlab_eval', sFiles, [], ...
    'matlab',      'Data = Data.^2;', ...
    'sensortypes', 'MEG', ...
    'overwrite',   0);

Export/Import with the database explorer

Right-click on the Deviant average in the database explorer > File > Export to Matlab > "DataMat".

Data exported as "DataMat"
>> DataMat
DataMat =
     ChannelFlag: [340x1 double]
    ColormapType: []
         Comment: 'Avg: deviant (39 files)'
        DataType: 'recordings'
          Device: 'CTF'
    DisplayUnits: []
               F: [340x361 double]
         History: {45x3 cell}
             Std: []
            Time: [1x361 double]
            nAvg: 39
          Events: [1x1 struct]

DataMat is the exact content of the corresponding .mat file, as loaded with Matlab's load() function. Edit some of the fields of this structure from the Matlab command window:

>> DataMat.Comment = 'Test square';
>> DataMat.F = DataMat.F .^ 2;

Now right-click on the folder containing the original file > File > Import from Matlab > DataMat:

If instead, you right-click on the original file and select the menu File > Import from Matlab, it overwrites the selected file instead of creating a new one with the selected structure.

Reference: File manipulation

Useful functions for manipulating file names and paths (read the code of the functions for help):

file_fullpath: Converts a relative file path to an absolute path.
file_short: Converts an absolute file path to a short path, relative to the current protocol folder.
file_gettype: Returns the type of a file.

Reading files from a script (all the functions take relative paths in input):

in_tess_bst(TessFile): Read a surface file.
in_mri_bst(MriFile): Read a MRI/volume file.
in_bst_data(DataFile): Read an imported epoch.
in_bst_timefreq(TimefreqFile): Read a power spectrum, time-frequency or connectivity file.
in_bst_channel(ChannelFile): Read a channel file.
in_bst_headmodel(HeadmodelFile, ApplyOrient): Read a head model file and apply orientations.
in_bst_results(ResultsFile, LoadFull): Load a source file and optionally reconstruct the full source time series on the fly (ImagingKernel * recordings).
in_bst_matrix(MatrixFile): Read a file with the type "matrix".
in_bst(FileName, TimeWindow): Read any Brainstorm data file with the possibility to load only a specific part of the file. "TimeWindow" is a range of time values in seconds: [tStart, tStop].
bst_process('LoadInputFile', FileName, Target, TimeWindow): The most high-level function for reading data files. "Target" is a string with the list of signal names or types to load.
bst_memory('GetConnectMatrix', TimefreqMat): Rebuild a full connectivity matrix.
in_fopen(DataFile, FileFormat, ImportOptions): Low-level function for opening continuous files.
in_fread(sFile, ChannelMat, iEpoch, SamplesBounds, iChannels, ImportOptions): Low-level function for reading blocks from continuous files. Requires a call to in_fopen first to get the sFile structure.

Saving files:

bst_save(FileName, FileMat, Version, isAppend): Save a file but does not register it in the database.
- FileName: Absolute path to a .mat file, use in combination with file_fullpath for relative paths.
- FileMat: Valid Brainstorm structure, corresponding to the file type.
- Version: Defines which version of the Matlab .mat format is used to store the data:
  - 'v6': Fastest option, bigger files, no compression, no files >2Gb
  - 'v7': Slower option, compressed, no files >2Gb
  - 'v7.3': Much slower than the others, compressed, but only way to save files > 2Gb.
- isAppend: If set to 1, updates only the fields defined in FileMat, keep the others untouched.
file_unique: Produces a unique file name by adding a number tag to it.
bst_process('GetNewFilename', OutputFolder, BaseFilename): Generate a new unique file name based on the beginning of the file name (eg. BaseFilename='data_average_test_').

Registering new files in the database:

db_add(iStudy/iSubject, FileMat): Add a new file in an anatomy folder or a functional data folder. This function saves the file and then reloads the folder. FileMat must be a structure, not a filename. You should not save the file manually before calling this function.
db_add_data(iStudy, FileName, FileMat): Register in the database a structure FileMat that has already been saved in file FileName. You should call bst_save manually before calling this function.
db_add_data(iStudy, FileName, FileMat, iItem): Overwrites the existing file #iItem.

Reload folders (if you saved or deleted files without registering correctly the modification in the database):

db_reload_studies(iStudies): Reload only the select data folders (aka "studies").
db_reload_conditions(iSubjects): Reload all the data folders for a subject.
db_reload_subjects(iSubjects): Reload the anatomy of the selected subjects.
db_reload_database('current'): Reload the entire protocol (anatomy and functional data).

Other useful database functions:

db_add_condition: Create a new folder in a subject.
db_add_subject: Create a new subject.
db_delete_studies: Delete a list of folders.
db_delete_subjects: Delete a list of subjects.
db_group_conditions: Merge two folders from the same subject.
db_rename_condition: Rename a folder.
db_rename_subject: Rename a subject.
db_set_channel: Set the channel file for a folder.
db_set_noisecov: Set the noise/data covariance for a folder, or copy to other folders/subjects.
db_set_template: Copy an anatomy template to a subject or use it as the default anatomy.

Export a file from the database to other file formats (read the comments in the functions for help):

export_channel
export_data
export_events
export_result
export_timefreq
export_matrix
export_mri
export_surfaces
export_protocol: Export a subject or an entire protocol as a .zip file.

Convert Brainstorm structures to FieldTrip structures:

out_fieldtrip_channel
out_fieldtrip_data
out_fieldtrip_timefreq
out_fieldtrip_headmodel
out_fieldtrip_results
out_fieldtrip_matrix

Reference: Display functions

Create new visualization figures:

view_channels: Display sensors in a 3D figure.
view_helmet: Display the inner surface of the MEG helmet in a 3D figure.
view_timeseries: Display a data file as time series.
view_timeseries_matrix: Display a custom matrix as time series.
view_topography: Display a data file as a spatial topography.
view_erpimage: Display multiple data files as an image, signal by signal.
view_timefreq: Open a time-frequency file (various display modes available).
view_spectrum: Display a power spectrum (PSD or time-frequency files).
view_connect: Open a connectivity matrix (various display modes available).
view_matrix: Open a "matrix" file (various display modes available).
view_contactsheet: Create a contact sheet in time or across a volume from an existing figure.
view_noisecov: Display a noise or data covariance file.
view_dipoles: Open a dipoles file (various display modes available).
view_pac: Open PAC results (various display modes available).
view_mri: View a MRI file in the MRI viewer (with or without a functional overlay from a source file).
view_mri_3d: View a MRI file in a 3D figure (with or without a functional overlay from a source file).
view_surface: View a surface.
view_surface_data: View a surface file with a source file as its texture.
view_surface_matrix: View a custom surface (user defines vertices, faces, color, transparency).
view_image_reg: Display a 3D or 4D matrix as an image with time and/or frequency dimensions.
view_struct: Display a structure as with the popup menu "File > View file contents".
script_view_sources: Shortcut script to display source files.
bst_memory('UnloadAll', 'Forced'): Close all the existing figures.

Configure time-series figures:

panel_time('SetCurrentTime', t): Set current time.
panel_record('SetTimeLength', duration): Set the length of the current display page, in seconds.
panel_record('SetStartTime', t): Set the start of the current page, in seconds.
panel_record('SetDisplayMode', hFig, DisplayMode): 'column' or 'butterfly'.
panel_filter('SetFilters', isLowPass, LowPass, isHighPass, HighPass, isSinRem, SinRem, isMirror)
panel_montage('SetCurrentMontage', hFig, MontageName): Change the montage of channels.
bst_figures('SetSelectedRows', SelectedChannels): Set selected channels (cell array of strings).
figure_timeseries('SetTimeSelectionManual', hFig, TimeWindow): Select a time segment.

Configure 3D figures:

figure_3d('SetStandardView', hFig, 'left'): Change camera view (top,bottom,left,right,front,back).
figure_3d('ViewSensors', hFig, isMarkers, isLabels): Enable the view of sensor markers and labels.
panel_surface('SetShowSulci', hFig, iTess, 1): Show/hide the sulci (darker color for deeper areas).
panel_surface('SetSurfaceColor', hFig, iTess, [1 0 0]): Set the surface color.
panel_surface('SetSurfaceSmooth', hFig, iTess, Smooth, 0): Set the amount of smoothing (0-1).
panel_surface('SetSurfaceTransparency', hFig, iTess, Transp): Set the surface transparency (0-1).
panel_surface('SetDataThreshold', hFig, iTess, Thresh): Set the amplitude threshold.
panel_surface('SetSizeThreshold', hFig, iTess, MinSize): Set size threshold (min size slider).
panel_surface('SelectHemispheres', target): Equivalent to clicking on the buttons in the Resect panel of the Surface tab. Possible target values: 'left', 'right', 'struct', 'none'
figure_mri('SetLocation', CsName, hFig, [], xyz): CsName=voxel/mri/scs/mni, xyz=[x,y,z]

Configure time-frequency figures:

panel_freq('SetCurrentFreq', iFreq, 1): Set the current frequency index (from the Freqs vector)
panel_freq('SetCurrentFreq', Freq, 0): Set the current frequency (in Hz).
sOptions = panel_display('GetDisplayOptions'): Get display options selected in the Display tab.
panel_display('SetDisplayOptions', sOptions): Change the options selected in the Display tab.
sOptions.HideEdgeEffects: Controls the checkbox "Hide edge effects" (0 or 1).
sOptions.HighResolution: Controls the checkbox "Smooth display" (0 or 1).
sOptions.RowName: Controls the signal that is currently displayed (for 'SingleSensor' display mode).
sOptions.Function: Controls the display function (magnitude, power, log, phase).

Configure colormaps:

bst_colormaps('SetColormapName', ColormapType, ColormapName): 'jet', 'parula', 'cmap_rbw', ...
bst_colormaps('SetMaxMode', ColormapType, MaxMode): Colorbar range ('global', 'local', 'custom').
bst_colormaps('SetMaxCustom', ColormapType, [], Min, Max): Set a custom colorbar range.
bst_colormaps('SetColormapAbsolute', ColormapType, isAbsolute): Show positive or relative values
bst_colormaps('SetDisplayColorbar', ColormapType, isDisplay): Show colorbar in the figures.
bst_colormaps('RestoreDefaults', ColormapType): Restore the default configuration for a colormap.
ColormapType: anatomy, meg, eeg, sources, stat1, stat2, time, timefreq, connect1, connectn, image

Configure statistical thresholding:

StatThreshOptions = bst_get('StatThreshOptions'): Get display options selected in the Stat tab.
bst_set('StatThreshOptions', StatThreshOptions): Change the options selected in the Stat tab.
StatThreshOptions.pThreshold: Current significance level α (ie. p-value threshold)
StatThreshOptions.Correction: Correction for multiple comparisons ('none', 'fdr', 'bonferroni')
StatThreshOptions.Control: List of dimensions to correct for multiple comparisons (default = [1 2 3])

Export the contents of a figure to a file:

out_figure_image: Screen capture of any Brainstorm figure.
out_figure_movie: Save a movie from one or multiple Brainstorm figures.
out_figure_timefreq: Extract some of the data displayed in a time-frequency figure.
out_figure_timeseries: Extract some of the data displayed in a time series figure.

Example: Creating a new file

This section illustrates how to add new files to the database. We will create a sinusoidal signal and save it in a "matrix" file, in a new folder of the subject "Test".

% Time: 1 second with a sampling frequency of 1000Hz
t = 0:0.001:1;
% Generate two sinsuoidal signals (20Hz,30Hz)
F = [sin(20*2*pi*t); 0.5*sin(30*2*pi*t)];

% Initialize an empty "matrix" structure
sMat = db_template('matrixmat');
% Fill the required fields of the structure
sMat.Value       = F;
sMat.Comment     = 'Test sinusoids';
sMat.Description = {'Signal #1: 20Hz'; 'Signal #2: 30Hz'};
sMat.Time        = t;

% Create a new folder "Script" in subject "Test"
iStudy = db_add_condition('Test', 'Script');
% Get the corresponding study structure
sStudy = bst_get('Study', iStudy);

There are many options to add a new file to the database, with various levels of requirements. You can call the db_add function (reloads the destination folder, therefore slow if you save many files), save the file in the corresponding folder and reload the protocol (slow as well), or register the file in the database manually (more complicated but faster).

Option #1: db_add

OutputFile = db_add(iStudy, sMat);

Option #2: bst_save / db_reload_studies

% Get the full path to the new folder
% (same folder as the brainstormstudy.mat file for this study)
OutputFolder = bst_fileparts(file_fullpath(sStudy.FileName));
% Get a new unique filename (including a timestamp)
MatrixFile = bst_process('GetNewFilename', OutputFolder, 'matrix_test');
% Save file
bst_save(MatrixFile, sMat, 'v6');
% Reload the folder in which the new file was saved
db_reload_studies(iStudy);

Option #3: bst_save / db_add_data

% Another way to generate a unique filename (without a timestamp)
MatrixFile = file_unique(bst_fullfile(OutputFolder, 'matrix_test.mat'));
% Save file
bst_save(MatrixFile, sMat, 'v6');
% Reference saved file in the database
db_add_data(iStudy, MatrixFile, sMat);
% Update the database explorer display
panel_protocols('UpdateNode', 'Study', iStudy);

Example: Editing events

A step that commonly requires manual changes is the definition of the event markers. For example, we have to combine external triggers or behavioral information with the existing events. This example illustrates how to load the events, modify them and save them back.

For the continuous recordings, the events are saved in the .mat file corresponding to the "Link to raw file". These structures contain only meta-data and information created with Brainstorm, the EEG/MEG recordings are available in a separate binary file. First, we need to load this link.

% Right-click on a "Link to raw file" in the database explorer
%  > File > Copy file path to clipboard
RawFile = '/.../@rawS01.../data_0raw_S01_..._01_600Hz_notch.mat'

% Load the "sFile" structure, contained in the .F structure
% of the link file (data_0raw...mat)
sRaw = in_bst_data(RawFile, 'F');

>> sRaw.F.events
ans =
1x7 struct array with fields:
    label
    color
    epochs
    times
    reactTimes
    select
    channels
    notes

For example, let's say we want to add 30ms to all the events in the category "button" in order to compensate for some hardware delay, and create a new event category with the modified timing. We need first to identify what is the index of the category "button", in this array of 7 event structures.

% Find the index of the event category "button"
iEvtButton = find(strcmpi({sRaw.F.events.label}, 'button'));

>> iEvtButton
iEvtButton =
     3

In the code above, note this special Matlab syntax that allows the concatenation of the values of one field across multiple structures, in an array of structures:

>> {sRaw.F.events.label}
ans =
    'standard'    'deviant'    'button'    'cardiac'
    'blink'    'bad_1-7Hz'    'bad_40-240Hz'

If you want to search instead all the events containing a specific tag, for example "bad", you can use the cellfun function (applies the same function sequentially to all the elements in a cell array and concatenates the results) in combination with the strfind function (search for a substring). The final call to the find function returns at which indices the list of tags found in the event label is not empty.

>> iEvtBad = find( ~cellfun( @(c)isempty(strfind(c,'bad')), ...
                             {sRaw.F.events.label}))
iEvtBad =
     6     7

The code below copies the existing event category "button", renames it and add a 30ms offset. If you add or remove events, you must adjust the size of the other fields: epochs (always 1 for most file formats), channels and notes (cell array of empty matrices in most cases).

% Copy the event category "button" to a new category
iEvtNew = length(sRaw.F.events) + 1;
sRaw.F.events(iEvtNew) = sRaw.F.events(iEvtButton);
% Rename the new event to "button_offset"
sRaw.F.events(iEvtNew).label = 'button_offset';

% How many samples in 30ms (0.030s * 600Hz = 18 samples)
offsetSample = round(0.030 .* sRaw.F.prop.sfreq);
% Apply offset to the events in the "button_offset" category
sRaw.F.events(iEvtNew).times = sRaw.F.events(iEvtNew).times + 0.03
% Round new time values to the nearest sample
sRaw.F.events(iEvtNew).times = ...
    round(sRaw.F.events(iEvtNew).times .* sRaw.F.prop.sfreq) ./ sRaw.F.prop.sfreq;
% Re-generate an epochs field with only ones, and empty notes and channels fields
% (optional here, as we didn't change the number of evt)
nTimes = size(sRaw.F.events(iEvtNew).times, 2);
sRaw.F.events(iEvtNew).epochs = ones(1, nTimes);
sRaw.F.events(iEvtNew).channels = cell(1, nTimes);
sRaw.F.events(iEvtNew).notes = cell(1, nTimes);
% Change the event color to yellow (red=1, green=1, blue=0)
sRaw.F.events(iEvtNew).color = [1 1 0];

>> sRaw.F.events(iEvtNew)
ans =
         label: 'button_offset'
         color: [1 1 0]
        epochs: [1x40 double]
         times: [1x40 double]
    reactTimes: []
        select: 1
      channels: {1x40 cell}
         notes: {1x40 cell}

The last step is to save the modifications back to the "Link to raw file". Here the call to file_fullpath is optional because the variable RawFile already contains the absolute path to the file.

% Update the sRaw structure to the RawFile file (the last parameter appends to the existing struct)
bst_save(file_fullpath(RawFile), sRaw, 'v6', 1);

Open the recordings to make sure your transformation worked the way you expected.

Find examples in the code

The easier way to understand how to use a function is to search the code with the "Find files" interface in Matlab. Go to the brainstorm3 folder, click on "Find files" (or Ctrl+Shift+F), enter the name of a function in "Find files containing text", Include subfolders, Match case. It will return all the lines that include the string you entered across all the files in the Brainstorm distribution. Just double-click on a line to jump to the code in the Matlab editor.

You can use the same interface to find what function is called when you click on a button or menu in the interface. Search for the label or the tooltip of the interface element in the same way. The example below shows how to track what happens when you click on the headmodel popup menu "Check spheres".

If you have trouble understanding how to set some input parameters, you can use the debugger to explore a real use case. Place a breakpoint at the begging of your function of interest (watch this tutorial if you don't know how to do this), for example in view_timeseries.m. Then click on the corresponding menus in the Brainstorm interface (eg. double-click on a data file). When the execution reaches the line you selected, it stops and gives you back the commands. You can explore the values in all the variables, modify them, and execute the code step by step (many options available in the Editor tab of Matlab).

Additional quality control

You can add in the reports all the information that may help you control the quality of the analysis, or figures you want to include in publications or clinical reports. The process "File > Save snapshot" lets you save some predefined views, but you can also custom screen captures. The example below shows how to add a "raster plot" for all the deviant trials from Run#01 in the report.

% Get all the deviant trials in Run#01  (the list includes the deviant average)
sDeviant = bst_process('CallProcess', 'process_select_files_data', [], [], ...
    'subjectname',   'Subject01', ...
    'condition',     'S01_AEF_20131218_01_600Hz_notch', ...
    'tag',           'deviant');

% Open raster plot
hFig = view_erpimage({sDeviant.FileName}, 'erpimage', 'MEG');
% Select the channel MRT34
sOptions = panel_display('GetDisplayOptions');
sOptions.RowName = 'MRT34';
panel_display('SetDisplayOptions', sOptions);

% Screen capture of this figure
% bst_report('Snapshot', hFig, FileName, Comment, WindowPosition);
bst_report('Snapshot', hFig, [], 'ERP image: MRT34', [300 100 600 400]);
% Close figure
close(hFig);

You can also add messages in the reports (information, warning or errors).

% Function call: bst_report(MsgType, sProcess, sInputs, Message)
bst_report('Info',    [], sDeviant, 'This is an information message.');
bst_report('Warning', [], sDeviant, 'This is a warning.');
bst_report('Error',   [], sDeviant, 'This is an error.');

% Open the report viewer to show the current report (not saved yet)
bst_report('Open', 'Current');

Report generated with the code above:

Loop over subjects

Creating loops is not supported yet by the script generator, but relatively easy to do from a script without knowing too much about Matlab programming. The example below shows how to create a loop over subjects to import their anatomy. The dataset used here is from the tutorial MEG visual: single subject.

With the Process1 box empty, select the process "Import > Import anatomy > Import anatomy folder" and generate a script. Simplify if using the guidelines presented in the previous sections:

% Input files
SubjectNames = {'sub001'};
RawFiles = {...
    '/.../Tutorials/sample_group/freesurfer/sub001'};

% Process: Import anatomy folder
bst_process('CallProcess', 'process_import_anatomy', [], [], ...
    'subjectname', SubjectNames{1}, ...
    'mrifile',     {RawFiles{1}, 'FreeSurfer'}, ...
    'nvertices',   15000);

Add the other subject names and corresponding FreeSurfer folders in the script header:

SubjectNames = {'sub001', 'sub002', 'sub003', 'sub004'};
RawFiles = {...
    '/.../Tutorials/sample_group/freesurfer/sub001', ...
    '/.../Tutorials/sample_group/freesurfer/sub002', ...
    '/.../Tutorials/sample_group/freesurfer/sub003', ...
    '/.../Tutorials/sample_group/freesurfer/sub004'};

Add a for loop around all the steps to repeat on each subject ("for" before, and "end" after the code), and replace the indices "1" with the loop variable:

% Loop on subjects
for iSubject = 1:length(SubjectNames)
    % Process: Import anatomy folder
    bst_process('CallProcess', 'process_import_anatomy', [], [], ...
        'subjectname', SubjectNames{iSubject}, ...
        'mrifile',     {RawFiles{iSubject}, 'FreeSurfer'}, ...
        'nvertices',   15000);
end

Loop over acquisition runs

If you have multiple subjects for which the anatomy is already imported, and multiple runs to process for each subject, you can add two nested for loops to link all the runs to the database in the same script. The dataset used here is from the tutorial MEG visual: single subject.

With the Process1 box empty, select the process "Import > Import recordings > Create link to raw file" and generate a script. Simplify if using the guidelines presented in the previous sections:

% Input files
SubjectNames = {'sub001'};
RawFiles = {...
    '/.../sample_group/ds117/sub001/MEG/run_01_sss.fif'};

% Process: Create link to raw file
sFileRaw = bst_process('CallProcess', 'process_import_data_raw', [], [], ...
    'subjectname',    SubjectNames{1}, ...
    'datafile',       {RawFiles{1}, 'FIF'}, ...
    'channelreplace', 0, ...
    'channelalign',   0, ...
    'evtmode',        'value');

Add the other subject names and all the runs for all the subjects (array of cell arrays) in the script header:

SubjectNames = {'sub001', 'sub002'};
RawFiles = {...
    {'/.../sample_group/ds117/sub001/MEG/run_01_sss.fif', ...
     '/.../sample_group/ds117/sub001/MEG/run_02_sss.fif', ...
     '/.../sample_group/ds117/sub001/MEG/run_03_sss.fif'}, ...
    {'/.../sample_group/ds117/sub002/MEG/run_01_sss.fif', ...
     '/.../sample_group/ds117/sub002/MEG/run_02_sss.fif', ...
     '/.../sample_group/ds117/sub002/MEG/run_03_sss.fif'}};

Add two for loops around the code to repeat on all the runs:

% Loop on subjects
for iSubject = 1:length(SubjectNames)
  % Loop on runs for each subject
  for iRun = 1:length(RawFiles{iSubject})
    % Process: Create link to raw file
    sFileRaw = bst_process('CallProcess', 'process_import_data_raw', [], [], ...
        'subjectname',    SubjectNames{iSubject}, ...
        'datafile',       {RawFiles{iSubjects}{iRun}, 'FIF'}, ...
        'channelreplace', 0, ...
        'channelalign',   0, ...
        'evtmode',        'value');
  end
end

How to process an entire study

This section proposes a standard workflow for processing a full group study with Brainstorm. It contains the same steps of analysis as the introduction tutorials, but separating what can be done automatically from what should be done manually. This workflow can be adapted to most ERP studies (stimulus-based).

Prototype: Start by processing one or two subjects completely interactively (exactly like in the introduction tutorials). Use the few pilot subjects that you have for your study to prototype the analysis pipeline and check manually all the intermediate stages. Take notes of what you're doing along the way, so that you can later write a script that reproduces the same operations.
Anatomical fiducials: Set NAS/LPA/RPA and compute the MNI transformation for each subject.
- Segmentation: Run FreeSurfer/BrainSuite to get surfaces and atlases for all the subjects.
- File > Batch MRI fiducials: This menu prompts for the selection of the fiducials for all the subjects and saves a file fiducials.m in each segmentation folder. You will not have to redo this even if you have to start over your analysis from the beginning.
- Script: Write a loop that calls the process "Import anatomy folder" for all the subjects.
- Alternatives: Create and import the subjects one by one and set the fiducials at the import time. Or use the default anatomy for all the subjects (or use warped templates).
Script #1: Pre-processing: Loop on the subjects and the acquisition runs.
- Create link to raw files: Link the subject and noise recordings to the database.
- Event markers: Read and group triggers from digital and analog channel, fix stimulation delays
- Evaluation: Power spectrum density of the recordings to evaluate their quality.
- Pre-processing: Notch filter, sinusoid removal, band-pass filter.
- Evaluation: Power spectrum density of the recordings to make sure the filters worked well.
- Cleanup: Delete the links to the original files (the filtered ones are copied in the database).
- Detect artifacts: Detect heartbeats, Detect eye blinks, Remove simultaneous.
- Compute SSP: Heartbeats, Blinks (this selects the first component of each decomposition)
- Compute ICA: If you have some artifacts you'd like to remove with ICA (no default selection).
- Screenshots: Check the MRI/sensors registration, PSD before and after corrections, SSP.
- Export the report: One report per subject, or one report for all the subjects, saved in HTML.
Manual inspection #1:
- Check the reports: Information messages (number of events, errors and warnings) and screen captures (registration problems, obvious noisy channels, incorrect SSP topographies).
- Mark bad channels: Open the recordings, select the channels and mark them as bad. Or use the process "Set bad channels" to mark the same bad channels in multiple files.
- Fix the SSP/ICA: For the suspicious runs: Open the file, adjust the list of blink and cardiac events, remove and recompute the SSP decompositions, manually select the components.
- Detect other artifacts: Run the process on all the runs of all the subjects at once (select all the files in Process1 and run the process, or generate the equivalent script).
- Mark bad segments: Review the artifacts detected in 1-7Hz and 40-240Hz, keep only the ones you really want to remove, then mark the event categories as bad. Review quickly the rest of the file and check that there are no other important artifacts.
- Additional SSP: If you find one type of artifact that repeats (typically saccades and SQUID jumps), you can create additional SSP projectors, either with the process "SSP: Generic" or directly from a topography figure (right-click on the figure > Snapshot> Use as SSP projector).
Script #2: Subject-level analysis: Epoching, averaging, sources, time-frequency.
- Importing: Process "Import MEG/EEG: Events" and "Pre-process > Remove DC offset".
- Averaging: Average trials by run, average runs by subject (registration problem in MEG).
- Noise covariance: Compute from empty room or resting recordings, copy to other folders.
- Head model: Compute for each run, or compute once and copy if the runs are co-registered.
- Sources: Compute for each run, average across runs and subjects in source space for MEG.
- Time-frequency: Computation with Hilbert transform or Morlet wavelets, then normalize.
- Screenshots: Check the quality of all the averages (time series, topographies, sources).
- Export the report: One report per subject, or one report for all the subjects, saved in HTML.
Manual inspection #2:
- Check the reports: Check the number of epochs imported and averaged in each condition, check the screen capture of the averages (all the primary responses should be clearly visible).
- Regions of interest: If not using predefined regions from an atlas, define the scouts on the anatomy of each subject (or on the template and then project them to the subjects).
Script #3: Group analysis, ROI-based analysis, etc.
- Averaging: Group averages for the sensor data, the sources and the time-frequency maps.
- Statistics: Contrast between conditions or groups of subjects.
- Regions of interest: Any operation that involve scouts.

Final scripts

The following script from the Brainstorm distribution reproduces the introduction tutorials ("Get started"): brainstorm3/toolbox/script/tutorial_introduction.m - Report: report_TutorialIntroduction.html

function tutorial_introduction(tutorial_dir, reports_dir)
% TUTORIAL_INTRODUCTION: Script that runs all the Brainstorm introduction tutorials.
%
% INPUTS: 
%    - tutorial_dir : Directory where the sample_introduction.zip file has been unzipped
%    - reports_dir  : Directory where to save the execution report (instead of displaying it)

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
% 
% Copyright (c)2000-2020 University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
% 
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
%
% For more information type "brainstorm license" at command prompt.
% =============================================================================@
%
% Author: Francois Tadel, 2016-2017


% ===== FILES TO IMPORT =====
% Output folder for reports
if (nargin < 2) || isempty(reports_dir) || ~isdir(reports_dir)
    reports_dir = [];
end
% You have to specify the folder in which the tutorial dataset is unzipped
if (nargin == 0) || isempty(tutorial_dir) || ~file_exist(tutorial_dir)
    error('The first argument must be the full path to the dataset folder.');
end
% Subject name
SubjectName = 'Subject01';
% Build the path of the files to import
AnatDir    = fullfile(tutorial_dir, 'sample_introduction', 'anatomy');
Run1File   = fullfile(tutorial_dir, 'sample_introduction', 'data', 'S01_AEF_20131218_01_600Hz.ds');
Run2File   = fullfile(tutorial_dir, 'sample_introduction', 'data', 'S01_AEF_20131218_02_600Hz.ds');
NoiseFile  = fullfile(tutorial_dir, 'sample_introduction', 'data', 'S01_Noise_20131218_02_600Hz.ds');
% Check if the folder contains the required files
if ~file_exist(Run1File)
    error(['The folder ' tutorial_dir ' does not contain the folder from the file sample_introduction.zip.']);
end
% Re-inialize random number generator
if (bst_get('MatlabVersion') >= 712)
    rng('default');
end


%% ===== TUTORIAL #1: CREATE PROTOCOL ================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #1: Create protocol' 10]);
% The protocol name has to be a valid folder name (no spaces, no weird characters...)
ProtocolName = 'TutorialIntroduction';
% Start brainstorm without the GUI
if ~brainstorm('status')
    brainstorm nogui
end
% Delete existing protocol
gui_brainstorm('DeleteProtocol', ProtocolName);
% Create new protocol
gui_brainstorm('CreateProtocol', ProtocolName, 0, 0);
% Start a new report
bst_report('Start');
% Reset colormaps
bst_colormaps('RestoreDefaults', 'meg');


%% ===== TUTORIAL #2: IMPORT ANATOMY =================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #2: Import anatomy' 10]);
% Process: Import FreeSurfer folder
bst_process('CallProcess', 'process_import_anatomy', [], [], ...
    'subjectname', SubjectName, ...
    'mrifile',     {AnatDir, 'FreeSurfer'}, ...
    'nvertices',   15000, ...
    'nas', [127, 213, 139], ...
    'lpa', [ 52, 113,  96], ...
    'rpa', [202, 113,  91]);
% This automatically calls the SPM registration procedure because the AC/PC/IH points are not defined



%% ===== TUTORIAL #3: EXPLORE ANATOMY ================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #3: Explore anatomy' 10]);
% Get subject definition
sSubject = bst_get('Subject', SubjectName);
% Get MRI file and surface files
MriFile    = sSubject.Anatomy(sSubject.iAnatomy).FileName;
CortexFile = sSubject.Surface(sSubject.iCortex).FileName;
HeadFile   = sSubject.Surface(sSubject.iScalp).FileName;
% Display MRI
hFigMri1 = view_mri(MriFile);
hFigMri3 = view_mri_3d(MriFile, [], [], 'NewFigure');
hFigMri2 = view_mri_slices(MriFile, 'x', 20); 
pause(0.5);
% Close figures
close([hFigMri1 hFigMri2 hFigMri3]);
% Display scalp and cortex
hFigSurf = view_surface(HeadFile);
hFigSurf = view_surface(CortexFile, [], [], hFigSurf);
hFigMriSurf = view_mri(MriFile, CortexFile);
% Figure configuration
iTess = 2;
panel_surface('SetShowSulci',     hFigSurf, iTess, 1);
panel_surface('SetSurfaceColor',  hFigSurf, iTess, [1 0 0]);
panel_surface('SetSurfaceSmooth', hFigSurf, iTess, 0.5, 0);
panel_surface('SetSurfaceTransparency', hFigSurf, iTess, 0.8);
figure_3d('SetStandardView', hFigSurf, 'left');
pause(0.5);
% Close figures
close([hFigSurf hFigMriSurf]);



%% ===== TUTORIAL #4: CHANNEL FILE ===================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #4: Channel file' 10]);
% Process: Create link to raw files
sFilesRun1 = bst_process('CallProcess', 'process_import_data_raw', [], [], ...
    'subjectname',  SubjectName, ...
    'datafile',     {Run1File, 'CTF'}, ...
    'channelalign', 1);
sFilesRun2 = bst_process('CallProcess', 'process_import_data_raw', [], [], ...
    'subjectname',  SubjectName, ...
    'datafile',     {Run2File, 'CTF'}, ...
    'channelalign', 1);
sFilesNoise = bst_process('CallProcess', 'process_import_data_raw', [], [], ...
    'subjectname',  SubjectName, ...
    'datafile',     {NoiseFile, 'CTF'}, ...
    'channelalign', 0);
sFilesRaw = [sFilesRun1, sFilesRun2, sFilesNoise];
% Process: Snapshot: Sensors/MRI registration
bst_process('CallProcess', 'process_snapshot', [sFilesRun1, sFilesRun2], [], ...
    'target',   1, ...  % Sensors/MRI registration
    'modality', 1, ...  % MEG (All)
    'orient',   1, ...  % left
    'Comment',  'MEG/MRI Registration');

% View sensors
hFig = view_surface(HeadFile);
hFig = view_channels(sFilesRun1.ChannelFile, 'MEG', 1, 1, hFig);
% Hide sensors
pause(0.5);
hFig = view_channels(sFilesRun1.ChannelFile, 'MEG', 0, 0, hFig);
% View coils
hFig = view_channels(sFilesRun1.ChannelFile, 'CTF', 1, 1, hFig);
% View helmet
pause(0.5);
hFig = view_helmet(sFilesRun1.ChannelFile, hFig);
pause(0.5);
close(hFig);
% Edit good/bad channel for current file
gui_edit_channel(sFilesRun1.ChannelFile);
pause(0.5);
% Unload everything
bst_memory('UnloadAll', 'Forced');



%% ===== TUTORIAL #5: REVIEW RAW =====================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #5: Review raw' 10]);
% Process: Convert to continuous (CTF): Continuous
bst_process('CallProcess', 'process_ctf_convert', sFilesRaw, [], ...
    'rectype', 2);  % Continuous

% View recordings
hFigMeg = view_timeseries(sFilesRun1.FileName, 'MEG');
hFigEeg = view_timeseries(sFilesRun1.FileName, 'Misc');
hFigSel = view_timeseries(sFilesRun1.FileName, 'MEG', {'MLT11','MLT12','MLT13'});
% Figure configuration
pause(0.5);
panel_record('SetTimeLength', 3);
panel_record('SetStartTime', 100);
panel_record('SetDisplayMode', hFigMeg, 'column');
panel_montage('SetCurrentMontage', hFigMeg, 'CTF LT');
% Set filters: panel_filter('SetFilters', LowPassEnabled, LowPassValue, HighPassEnabled, HighPassValue, SinRemovalEnabled, SinRemovalValue, MirrorEnabled, FullSourcesEnabled)
panel_filter('SetFilters', 1, 100, 1, 1, 0, [], 0, 0);
pause(0.5);
panel_record('SetDisplayMode', hFigMeg, 'butterfly');
panel_montage('SetCurrentMontage', hFigMeg, '');
% Close figures
close([hFigMeg hFigEeg hFigSel]);



%% ===== TUTORIAL #8: STIM DELAYS ====================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #8: Stim delays' 10]);
% Process: Detect: standard_fix
bst_process('CallProcess', 'process_evt_detect_analog', [sFilesRun1, sFilesRun2], [], ...
    'eventname',   'standard_fix', ...
    'channelname', 'UADC001', ...
    'timewindow',  [], ...
    'threshold',   1.2, ...
    'blanking',    0.2, ...
    'highpass',    0, ...
    'lowpass',     0, ...
    'refevent',    'standard', ...
    'isfalling',   0, ...
    'ispullup',    0, ...
    'isclassify',  0);
% Process: Detect: deviant_fix
bst_process('CallProcess', 'process_evt_detect_analog', [sFilesRun1, sFilesRun2], [], ...
    'eventname',   'deviant_fix', ...
    'channelname', 'UADC001', ...
    'timewindow',  [], ...
    'threshold',   1.2, ...
    'blanking',    0.2, ...
    'highpass',    0, ...
    'lowpass',     0, ...
    'refevent',    'deviant', ...
    'isfalling',   0, ...
    'ispullup',    0, ...
    'isclassify',  0);
% Process: Read from channel
bst_process('CallProcess', 'process_evt_read', [sFilesRun1, sFilesRun2], [], ...
    'stimchan',  'UDIO001', ...
    'trackmode', 1, ...  % Value: detect the changes of channel value
    'zero',      0);

% Process: Delete events
bst_process('CallProcess', 'process_evt_delete', [sFilesRun1, sFilesRun2], [], ...
    'eventname', 'standard, deviant, button');
% Process: Rename event (standard_fix>standard)
bst_process('CallProcess', 'process_evt_rename', [sFilesRun1, sFilesRun2], [], ...
    'src',  'standard_fix', ...
    'dest', 'standard');
% Process: Rename event (deviant_fix>deviant)
bst_process('CallProcess', 'process_evt_rename', [sFilesRun1, sFilesRun2], [], ...
    'src',  'deviant_fix', ...
    'dest', 'deviant');
% Process: Rename event (64>button)
bst_process('CallProcess', 'process_evt_rename', [sFilesRun1, sFilesRun2], [], ...
    'src',  '64', ...
    'dest', 'button');



%% ===== TUTORIAL #10: FREQUENCY FILTERS =============================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #10: Frequency filters' 10]);
% Process: Sinusoid removal: 60Hz 120Hz 180Hz 300Hz
sFilesNotch = bst_process('CallProcess', 'process_notch', sFilesRaw, [], ...
    'freqlist',    [60, 120, 180], ...
    'sensortypes', 'MEG', ...
    'read_all',    0);
% Process: Power spectrum density (Welch)
sFilesPsd = bst_process('CallProcess', 'process_psd', [sFilesRaw, sFilesNotch], [], ...
    'timewindow',  [], ...
    'win_length',  4, ...
    'win_overlap', 50, ...
    'clusters',    {}, ...
    'sensortypes', 'MEG', ...
    'edit', struct(...
         'Comment',    'Power', ...
         'TimeBands',  [], ...
         'Freqs',      [], ...
         'ClusterFuncTime', 'none', ...
         'Measure',    'power', ...
         'Output',     'all', ...
         'SaveKernel', 0));
% Process: Snapshot: Frequency spectrum
bst_process('CallProcess', 'process_snapshot', sFilesPsd, [], ...
    'target',   10, ...  % Frequency spectrum
    'modality', 1, ...   % MEG (All)
    'Comment',  'Power spectrum density');
% Process: Delete folders
bst_process('CallProcess', 'process_delete', sFilesRaw, [], ...
    'target', 2);  % Delete folders
% Separate the three outputs
sFilesRun1  = {sFilesNotch(1).FileName};
sFilesRun2  = {sFilesNotch(2).FileName};
sFilesNoise = {sFilesNotch(3).FileName};



%% ===== TUTORIAL #11: BAD CHANNELS ==================================================
%  ===================================================================================
% % Process: Set bad channels
% sFiles = bst_process('CallProcess', 'process_channel_setbad', sFilesRun2, [], ...
%     'sensortypes', 'MRT51, MLO52, MLO42, MLO43');



%% ===== TUTORIAL #12: ARTIFACTS DETECTION ===========================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #12: Artifacts detection' 10]);
% Process: Detect heartbeats
bst_process('CallProcess', 'process_evt_detect_ecg', [sFilesRun1, sFilesRun2], [], ...
    'channelname', 'ECG', ...
    'timewindow',  [], ...
    'eventname',   'cardiac');
% Process: Detect eye blinks
bst_process('CallProcess', 'process_evt_detect_eog',  [sFilesRun1, sFilesRun2], [], ...
    'channelname', 'VEOG', ...
    'timewindow',  [], ...
    'eventname',   'blink');
% Process: Remove simultaneous
bst_process('CallProcess', 'process_evt_remove_simult', [sFilesRun1, sFilesRun2], [], ...
    'remove', 'cardiac', ...
    'target', 'blink', ...
    'dt',     0.25, ...
    'rename', 0);



%% ===== TUTORIAL #13: SSP ===========================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #13: SSP' 10]);
% Process: SSP ECG: cardiac
bst_process('CallProcess', 'process_ssp_ecg', [sFilesRun1, sFilesRun2], [], ...
    'eventname',   'cardiac', ...
    'sensortypes', 'MEG', ...
    'usessp',      0, ...
    'select',      1);
% Process: SSP EOG: blink
bst_process('CallProcess', 'process_ssp_eog', sFilesRun1, [], ...
    'eventname',   'blink', ...
    'sensortypes', 'MEG', ...
    'usessp',      0, ...
    'select',      [1 2]);
bst_process('CallProcess', 'process_ssp_eog', sFilesRun2, [], ...
    'eventname',   'blink', ...
    'sensortypes', 'MEG', ...
    'usessp',      0, ...
    'select',      1);


%% ===== TUTORIAL #14: BAD SEGMENTS ==================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #14: Bad segments' 10]);
% Process: Detect other artifacts
bst_process('CallProcess', 'process_evt_detect_badsegment', [sFilesRun1, sFilesRun2], [], ...
    'timewindow',  [], ...
    'sensortypes', 'MEG', ...
    'threshold',   3, ...  % 3
    'isLowFreq',   1, ...
    'isHighFreq',  1);

% Process: Rename event (1-7Hz > saccade)  (Run02 only)
bst_process('CallProcess', 'process_evt_rename', sFilesRun2, [], ...
    'src',  '1-7Hz', ...
    'dest', 'saccade');

% Manual selection of saccades (cannot be done from the pipeline editor: manual edition of the structures)
sMatRun2 = in_bst_data(sFilesRun2{1}, 'F');
iEvtSaccade = find(strcmpi({sMatRun2.F.events.label}, 'saccade'));
sMatRun2.F.events(iEvtSaccade).times   = [30, 81.5, 104, 142.5, 167, 187.5, 246.5, 319;  31, 83, 105, 144, 168, 188.5, 248, 320];
sMatRun2.F.events(iEvtSaccade).epochs  = ones(1, size(sMatRun2.F.events(iEvtSaccade).times, 2));
sMatRun2.F.events(iEvtSaccade).channels = cell(1, size(sMatRun2.F.events(iEvtSaccade).times, 2));
sMatRun2.F.events(iEvtSaccade).notes    = cell(1, size(sMatRun2.F.events(iEvtSaccade).times, 2));
bst_save(file_fullpath(sFilesRun2{1}), sMatRun2, 'v6', 1);

% Process: SSP: saccade  (Run02 only)
bst_process('CallProcess', 'process_ssp', sFilesRun2, [], ...
    'timewindow',  [], ...
    'eventname',   'saccade', ...
    'eventtime',   [-0.2, 0.2], ...
    'bandpass',    [1.5, 7], ...
    'sensortypes', 'MEG', ...
    'usessp',      1, ...
    'saveerp',     0, ...
    'method',      1, ...
    'select',      1);
% Process: Detect other artifacts  (Run02 only)
bst_process('CallProcess', 'process_evt_detect_badsegment', sFilesRun2, [], ...
    'timewindow',  [], ...
    'sensortypes', 'MEG', ...
    'threshold',   3, ...  % 3
    'isLowFreq',   1, ...
    'isHighFreq',  1);

% Process: Rename event (1-7Hz > bad_1-7Hz)
bst_process('CallProcess', 'process_evt_rename', [sFilesRun1, sFilesRun2], [], ...
    'src',  '1-7Hz', ...
    'dest', 'bad_1-7Hz');
% Process: Rename event (40-240Hz > bad_40-240Hz)
bst_process('CallProcess', 'process_evt_rename', [sFilesRun1, sFilesRun2], [], ...
    'src',  '40-240Hz', ...
    'dest', 'bad_40-240Hz');
% Process: Snapshot: SSP projectors
bst_process('CallProcess', 'process_snapshot', [sFilesRun1, sFilesRun2], [], ...
    'target',  2, ...  % SSP projectors
    'Comment', 'SSP projectors');



%% ===== TUTORIAL #15: IMPORT EVENTS =================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #15: Import events' 10]);
% Process: Import MEG/EEG: Events (Run01)
sFilesEpochs1 = bst_process('CallProcess', 'process_import_data_event', sFilesRun1, [], ...
    'subjectname', SubjectName, ...
    'condition',   '', ...
    'eventname',   'standard, deviant', ...
    'timewindow',  [], ...
    'epochtime',   [-0.100, 0.500], ...
    'createcond',  0, ...
    'ignoreshort', 1, ...
    'usectfcomp',  1, ...
    'usessp',      1, ...
    'freq',        [], ...
    'baseline',    [-0.1, -0.0017]);
% Process: Import MEG/EEG: Events (Run02)
sFilesEpochs2 = bst_process('CallProcess', 'process_import_data_event', sFilesRun2, [], ...
    'subjectname', SubjectName, ...
    'condition',   '', ...
    'eventname',   'standard, deviant', ...
    'timewindow',  [], ...
    'epochtime',   [-0.100, 0.500], ...
    'createcond',  0, ...
    'ignoreshort', 1, ...
    'usectfcomp',  1, ...
    'usessp',      1, ...
    'freq',        [], ...
    'baseline',    [-0.1, -0.0017]);
% Display raster plot
hFigRaster = view_erpimage({sFilesEpochs1.FileName}, 'erpimage', 'MEG');
panel_display();
bst_report('Snapshot', hFigRaster, sFilesEpochs1(1).FileName, 'ERP image');
close(hFigRaster);


%% ===== TUTORIAL #16: AVERAGE =======================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #16: Average' 10]);
% Process: Average: By trial group (folder average)
sFilesAvg = bst_process('CallProcess', 'process_average', [sFilesEpochs1, sFilesEpochs2], [], ...
    'avgtype',    5, ...  % By trial groups (folder average)
    'avg_func',   1, ...  % Arithmetic average: mean(x)
    'weighted',   0, ...
    'keepevents', 1);
% Process: Delete events 'cardiac'
bst_process('CallProcess', 'process_evt_delete', sFilesAvg, [], ...
    'eventname', 'cardiac');
% Process: Snapshot: Recordings time series
bst_process('CallProcess', 'process_snapshot', sFilesAvg, [], ...
    'target',     5, ...  % Recordings time series
    'modality',   1, ...  % MEG (All)
    'Comment',    'Evoked response');
% Set colormap: global color scale
bst_colormaps('SetMaxMode', 'meg', 'global');
% Process: Snapshot: Recordings topography (contact sheet)
bst_process('CallProcess', 'process_snapshot', sFilesAvg, [], ...
    'target',         7, ...  % Recordings topography (contact sheet)
    'modality',       1, ...  % MEG
    'contact_time',   [0, 0.350], ...
    'contact_nimage', 15, ...
    'Comment',        'Evoked response');

% Process: Average+Stderr: By trial group (subject average)
sFilesAvgAll = bst_process('CallProcess', 'process_average', [sFilesEpochs1, sFilesEpochs2], [], ...
    'avgtype',    6, ...  % By trial group (subject average)
    'avg_func',   7, ...  % Arithmetic average + Standard error
    'weighted',   0, ...
    'keepevents', 1);
% Process: Delete events 'cardiac'
bst_process('CallProcess', 'process_evt_delete', sFilesAvgAll, [], ...
    'eventname', 'cardiac');
% Process: Delete events 'saccade'
bst_process('CallProcess', 'process_evt_delete', sFilesAvgAll, [], ...
    'eventname', 'saccade');
% Process: Snapshot: Recordings time series
bst_process('CallProcess', 'process_snapshot', sFilesAvgAll, [], ...
    'target',     5, ...  % Recordings time series
    'modality',   1, ...  % MEG (All)
    'Comment',    'Evoked response');


%% ===== TUTORIAL #17: EXPLORATION ===================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #17: Bad segments' 10]);
% View averages
hFigMeg1  = view_timeseries(sFilesAvg(1).FileName, 'MEG');
hFigMeg2  = view_timeseries(sFilesAvg(2).FileName, 'MEG');
hFigEeg1  = view_timeseries(sFilesAvg(1).FileName, 'Misc');
hFigEeg2  = view_timeseries(sFilesAvg(2).FileName, 'Misc');
hFigTopo1 = view_topography(sFilesAvg(1).FileName, 'MEG', '2DSensorCap');
hFigTopo2 = view_topography(sFilesAvg(2).FileName, 'MEG', '2DSensorCap');
hFigTp2   = view_topography(sFilesAvg(3).FileName, 'MEG', '3DSensorCap');
hFigTp3   = view_topography(sFilesAvg(3).FileName, 'MEG', '2DDisc');
hFigTp4   = view_topography(sFilesAvg(3).FileName, 'MEG', '2DLayout');
% Set time: 90ms
panel_time('SetCurrentTime', 0.090);
% Set filters: 40Hz low-pass, no high-pass
panel_filter('SetFilters', 1, 40, 0, [], 0, [], 0, 0);
% View selected sensors
SelectedChannels = {'MLC31', 'MLC32'};
bst_figures('SetSelectedRows', SelectedChannels);
view_timeseries(sFilesAvg(4).FileName, [], SelectedChannels);
% Select time window
figure_timeseries('SetTimeSelectionManual', hFigMeg1, [0.070, 0.130]);
% Show sensors on 2DSensorCap topography
isMarkers = 1;
isLabels = 0;
figure_3d('ViewSensors', hFigTopo1, isMarkers, isLabels);
% Display time contact sheet for a figure
pause(0.5);
hContactFig = view_contactsheet( hFigTopo2, 'time', 'fig', [], 12, [0 0.120] );
pause(0.5);
close(hContactFig);



%% ===== TUTORIAL #18: COLORMAPS =====================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #18: Colormaps' 10]);
% Set 'Meg' colormap to 'jet'
bst_colormaps('SetColormapName', 'meg', 'jet');
pause(0.5);
% Set 'Meg' colormap to 'rwb'
bst_colormaps('SetColormapName', 'meg', 'cmap_rbw');
% Set colormap to display absolute values
bst_colormaps('SetColormapAbsolute', 'meg', 1);
% Normalize colormap for each time frame
bst_colormaps('SetMaxMode', 'meg', 'local');
% Hide colorbar
bst_colormaps('SetDisplayColorbar', 'meg', 0);
pause(0.5);
% Restore colormap to default values
bst_colormaps('RestoreDefaults', 'meg');
% Edit good/bad channel for current file
gui_edit_channelflag(sFilesAvg(1).FileName);
% Close figures
pause(0.5);
bst_memory('UnloadAll', 'Forced');



%% ===== TUTORIAL #20: HEAD MODEL ====================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #20: Head model' 10]);
% Process: Compute head model
bst_process('CallProcess', 'process_headmodel', sFilesAvg, [], ...
    'comment',      '', ...
    'sourcespace',  1, ...
    'meg',          3);  % Overlapping spheres
% Get study structure
sStudy = bst_get('Study', sFilesAvg(1).iStudy);
% Show spheres
hFig = view_spheres(sStudy.HeadModel(sStudy.iHeadModel).FileName, sStudy.Channel.FileName, sSubject);
pause(0.5);
close(hFig);



%% ===== TUTORIAL #21: NOISE COVARIANCE ==============================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #21: Noise covariance' 10]);
% Process: Compute covariance (noise or data)
bst_process('CallProcess', 'process_noisecov', sFilesNoise, [], ...
    'baseline',       [], ...
    'sensortypes',    'MEG, EEG, SEEG, ECOG', ...
    'target',         1, ...  % Noise covariance     (covariance over baseline time window)
    'dcoffset',       1, ...  % Block by block, to avoid effects of slow shifts in data
    'identity',       0, ...
    'copycond',       1, ...
    'copysubj',       0, ...
    'replacefile',    1);  % Replace
% Process: Snapshot: Noise covariance
bst_process('CallProcess', 'process_snapshot', sFilesNoise, [], ...
    'target',  3, ...  % Noise covariance
    'Comment', 'Noise covariance');

% Process: Compute covariance (noise or data)  [Run01]
bst_process('CallProcess', 'process_noisecov', sFilesEpochs1, [], ...
    'baseline',       [-0.1, -0.0017], ...
    'datatimewindow', [0, 0.5], ...
    'sensortypes',    'MEG, EEG, SEEG, ECOG', ...
    'target',         2, ...  % Data covariance      (covariance over data time window)
    'dcoffset',       1, ...  % Block by block, to avoid effects of slow shifts in data
    'identity',       0, ...
    'copycond',       0, ...
    'copysubj',       0, ...
    'replacefile',    1);  % Replace
% Process: Compute covariance (noise or data)  [Run02]
bst_process('CallProcess', 'process_noisecov', sFilesEpochs2, [], ...
    'baseline',       [-0.1, -0.0017], ...
    'datatimewindow', [0, 0.5], ...
    'sensortypes',    'MEG, EEG, SEEG, ECOG', ...
    'target',         2, ...  % Data covariance      (covariance over data time window)
    'dcoffset',       1, ...  % Block by block, to avoid effects of slow shifts in data
    'identity',       0, ...
    'copycond',       0, ...
    'copysubj',       0, ...
    'replacefile',    1);  % Replace
% Process: Snapshot: Data covariance
bst_process('CallProcess', 'process_snapshot', [sFilesEpochs1(1), sFilesEpochs2(1)], [], ...
    'target',  12, ...  % Data covariance
    'Comment', 'Data covariance');



%% ===== TUTORIAL #22: SOURCE ESTIMATION =============================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #22: Source estimation' 10]);
% === GET DEVIANT AVERAGE RUN01 ===
% Process: Select recordings in: Subject01/S01_AEF_20131218_01_600Hz_notch
sFiles01 = bst_process('CallProcess', 'process_select_files_data', [], [], ...
    'subjectname', SubjectName, ...
    'condition',   'S01_AEF_20131218_01_600Hz_notch', ...
    'includebad',  0);
% Process: Select file comments with tag: deviant
sFilesAvgDeviant01 = bst_process('CallProcess', 'process_select_tag', sFiles01, [], ...
    'tag',    'Avg: deviant', ...
    'search', 2, ...  % Search the file comments
    'select', 1);     % Select only the files with the tag

% === CONSTRAINED EXAMPLE ===
% Minimum norm options
InverseOptions = struct(...
    'Comment',        'MN: MEG', ...
    'InverseMethod',  'minnorm', ...
    'InverseMeasure', 'amplitude', ...
    'SourceOrient',   {{'fixed'}}, ...
    'Loose',          0.2, ...
    'UseDepth',       1, ...
    'WeightExp',      0.5, ...
    'WeightLimit',    10, ...
    'NoiseMethod',    'reg', ...
    'NoiseReg',       0.1, ...
    'SnrMethod',      'fixed', ...
    'SnrRms',         0.001, ...
    'SnrFixed',       3, ...
    'ComputeKernel',  1, ...
    'DataTypes',      {{'MEG'}});
% Process: Compute sources [2018]
sFilesSrcDeviant01 = bst_process('CallProcess', 'process_inverse_2018', sFilesAvgDeviant01, [], ...
    'output',  2, ...  % Kernel only: one per file
    'inverse', InverseOptions);

% === DISPLAY SOURCES MANUALLY ===
% View time series
hFigSrc1 = view_timeseries(sFilesAvgDeviant01(1).FileName, 'MEG');
% View on the cortex surface
hFigSrc2 = script_view_sources(sFilesSrcDeviant01.FileName, 'cortex');
% Set current time to 90ms
panel_time('SetCurrentTime', 0.090);
% Set orientation
figure_3d('SetStandardView', hFigSrc2, 'left');
% Set surface threshold
iSurf = 1;
thresh = .30; 
panel_surface('SetDataThreshold', hFigSrc2, iSurf, thresh);
% Set surface smoothing
panel_surface('SetSurfaceSmooth', hFigSrc2, iSurf, .6, 0);
% Show sulci
panel_surface('SetShowSulci', hFigSrc2, iSurf, 1);

% View sources on MRI (3D orthogonal slices)
hFigSrc3 = script_view_sources(sFilesSrcDeviant01.FileName, 'mri3d');
panel_surface('SetDataThreshold', hFigSrc3, iSurf, thresh);
% Set the position of the cuts in the 3D figure
cutsPosVox = [74 93 159];
panel_surface('PlotMri', hFigSrc3, cutsPosVox);

% View sources with MRI Viewer
hFigSrc4 = script_view_sources(sFilesSrcDeviant01.FileName, 'mriviewer');
panel_surface('SetDataThreshold', hFigSrc4, iSurf, thresh);
% Set the position of the cuts in the MRI Viewer (values in millimeters)
figure_mri('SetLocation', 'voxel', hFigSrc4, [], cutsPosVox);
% Close figures
close([hFigSrc1 hFigSrc2 hFigSrc3 hFigSrc4]);

% === UNCONSTRAINED EXAMPLE ===
% Unconstrained minnorm
InverseOptions.Comment        = 'MN: MEG';
InverseOptions.InverseMeasure = 'amplitude';
InverseOptions.SourceOrient   = {'free'};
% Process: Compute sources [2018]
sFilesSrcUnconst = bst_process('CallProcess', 'process_inverse_2018', sFilesAvgDeviant01, [], ...
    'output',  2, ...  % Kernel only: one per file
    'inverse', InverseOptions);


% === NORMALIZED SOURCES ===
% dSPM
InverseOptions.Comment        = 'dSPM: MEG';
InverseOptions.InverseMeasure = 'dspm2018';
InverseOptions.SourceOrient   = {'fixed'};
sFilesSrcDspm = bst_process('CallProcess', 'process_inverse_2018', sFilesAvgDeviant01, [], ...
    'output',  2, ...  % Kernel only: one per file
    'inverse', InverseOptions);
% sLORETA (old function)
sFilesSrcSloreta = bst_process('CallProcess', 'process_inverse', sFilesAvgDeviant01, [], ...
    'comment', '', ...
    'method',  3, ...  % sLORETA
    'wmne', struct(...
         'SourceOrient', {{'fixed'}}, ...
         'loose',        0.2, ...
         'SNR',          3, ...
         'pca',          1, ...
         'diagnoise',    0, ...
         'regnoise',     1, ...
         'magreg',       0.1, ...
         'gradreg',      0.1, ...
         'depth',        1, ...
         'weightexp',    0.5, ...
         'weightlimit',  10), ...
    'sensortypes', 'MEG, MEG MAG, MEG GRAD, EEG', ...
    'output', 2);  % Kernel only: one per file
% Process: Z-score normalization: [-100ms,-2ms]
sFilesSrcZscore = bst_process('CallProcess', 'process_baseline_norm', sFilesSrcDeviant01, [], ...
    'baseline',   [-0.100, -0.002], ...
    'source_abs', 0, ...
    'method',     'zscore');   % Z-score transformation:    x_std = (x - μ) / σ

% Process: Snapshot: Sources (one time)
bst_process('CallProcess', 'process_snapshot', sFilesSrcDeviant01, [], ...
    'target',    8, ...  % Sources (one time)
    'orient',    1, ...  % left
    'time',      0.09, ...
    'threshold', 30, ...
    'Comment',   'Current density map (Constrained)');
bst_process('CallProcess', 'process_snapshot', sFilesSrcDspm, [], ...
    'target',    8, ...  % Sources (one time)
    'orient',    1, ...  % left
    'time',      0.09, ...
    'threshold', 60, ...
    'Comment',   'dSPM');
bst_process('CallProcess', 'process_snapshot', sFilesSrcSloreta, [], ...
    'target',    8, ...  % Sources (one time)
    'orient',    1, ...  % left
    'time',      0.09, ...
    'threshold', 60, ...
    'Comment',   'sLORETA');
bst_process('CallProcess', 'process_snapshot', sFilesSrcZscore, [], ...
    'target',    8, ...  % Sources (one time)
    'orient',    1, ...  % left
    'time',      0.09, ...
    'threshold', 60, ...
    'Comment',   'Z-score');
bst_process('CallProcess', 'process_snapshot', sFilesSrcUnconst, [], ...
    'target',         8, ...  % Sources (one time)
    'orient',         1, ...  % left
    'time',           0.0917, ...
    'threshold',      0, ...
    'Comment',        'Current density map (Unconstrained)');

% === DELETE EXPERIMENTS ===
% Process: Delete constrained example
bst_process('CallProcess', 'process_delete', [sFilesSrcDeviant01, sFilesSrcDspm, sFilesSrcSloreta, sFilesSrcZscore, sFilesSrcUnconst], [], ...
    'target', 1);  % Delete selected files


% === SHARED KERNEL ===
% Constrained minnorm
InverseOptions.Comment        = 'MN: MEG';
InverseOptions.InverseMeasure = 'amplitude';
InverseOptions.SourceOrient   = {'fixed'};
% Process: Compute sources [2018]
sFilesAvgSrc = bst_process('CallProcess', 'process_inverse_2018', sFilesAvg, [], ...
    'output',  1, ...  % Kernel only: shared
    'inverse', InverseOptions);


% === AVERAGE SOURCES ACROSS RUNS ===
% Process: Average: By trial group (subject average)
sFilesIntraSrc = bst_process('CallProcess', 'process_average', sFilesAvgSrc, [], ...
    'avgtype',         6, ...  % By trial group (subject average)
    'avg_func',        1, ...  % Arithmetic average:  mean(x)
    'weighted',        1, ...
    'scalenormalized', 0);
% Process: Low-pass:40Hz
sFilesIntraSrcLow = bst_process('CallProcess', 'process_bandpass', sFilesIntraSrc, [], ...
    'highpass',    0, ...
    'lowpass',     40, ...
    'attenuation', 'strict', ...  % 60dB
    'mirror',      0, ...
    'overwrite',   0);
% Process: Z-score normalization: [-100ms,-2ms]
sFilesIntraZscore = bst_process('CallProcess', 'process_baseline_norm', sFilesIntraSrcLow, [], ...
    'baseline',   [-0.100, -0.0017], ...
    'source_abs', 0, ...
    'method',     'zscore');  % Z-score transformation:    x_std = (x - μ) / σ

% Process: Delete intermediate results
bst_process('CallProcess', 'process_delete', sFilesIntraSrcLow, [], ...
    'target', 1);  % Delete selected files
% Screen captures
bst_process('CallProcess', 'process_snapshot', sFilesIntraZscore, [], ...
    'target',    8, ...  % Sources (one time)
    'orient',    1, ...  % left
    'time',      0.09, ...
    'threshold', 40, ...
    'Comment',   'Average across runs (left)');
bst_process('CallProcess', 'process_snapshot', sFilesIntraZscore, [], ...
    'target',    8, ...  % Sources (one time)
    'orient',    2, ...  % right
    'time',      0.09, ...
    'threshold', 40, ...
    'Comment',   'Average across runs (right)');
bst_process('CallProcess', 'process_snapshot', sFilesIntraZscore(1), [], ...
    'target',         9, ...  % Sources (contact sheet)
    'orient',         1, ...  % left
    'contact_time',   [0, 0.35], ...
    'contact_nimage', 15, ...
    'threshold',      20, ...
    'Comment',        'Average across runs');


%% ===== TUTORIAL #23: SCOUTS ========================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #23: Scouts' 10]);
% Load surface file
sCortex = in_tess_bst(CortexFile);
% Add new scouts in first atlas
sCortex.iAtlas = find(strcmpi({sCortex.Atlas.Name}, 'Destrieux'));
% Save file
bst_save(file_fullpath(CortexFile), sCortex, 'v7');
% Unload everything
bst_memory('UnloadAll', 'Forced');
% Find scouts indices to display: {'A1L', 'A1R', 'IFGL', 'M1L'}
[tmp,iScouts,tmp] = intersect({sCortex.Atlas(sCortex.iAtlas).Scouts.Label}, {'G_temp_sup-G_T_transv L', 'G_temp_sup-G_T_transv R', 'G_front_inf-Opercular L', 'G_precentral L'});

% View cortex
hFigSurf1 = view_surface(CortexFile, [], [], 'NewFigure');
hFigSurf2 = view_surface(CortexFile, [], [], 'NewFigure');
figure_3d('SetStandardView', hFigSurf1, 'left');
figure_3d('SetStandardView', hFigSurf2, 'right');
panel_surface('SetSurfaceSmooth', hFigSurf1, 1, .6, 0);
panel_surface('SetSurfaceSmooth', hFigSurf2, 1, .6, 0);
panel_surface('SetShowSulci', hFigSurf1, 1, 1);
panel_surface('SetShowSulci', hFigSurf2, 1, 1);
% Configure scouts display
panel_scout('SetScoutsOptions', 0, 1, 1, 'all', 0.7, 1, 1, 0);
% View scouts
hFigScouts = view_scouts({sFilesIntraZscore.FileName}, iScouts);
hLegend = findobj(hFigScouts, 'Type', 'legend');
if ~isempty(hLegend) && ishandle(hLegend(1))
    set(hLegend(1), 'Units', 'pixels');
    pos = get(hLegend(1), 'Position');
    set(hLegend(1), 'Position', [1, 1, pos(3), pos(4)]);
end
% Save figures
bst_report('Snapshot', hFigScouts, sFilesIntraZscore(1).FileName, 'Scouts', [100 100 670 250]);
% Close all
pause(1);
bst_memory('UnloadAll', 'Forced');



%% ===== TUTORIAL #24: TIME-FREQUENCY ================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #24: Time-frequency' 10]);
% Process: Simulate generic signals
sSim = bst_process('CallProcess', 'process_simulate_matrix', [], [], ...
    'subjectname', 'Test', ...
    'condition',   'Simulation', ...
    'samples',     6000, ...
    'srate',       1000, ...
    'matlab',      ['f1 = 2; f2 = 20; f3 = 50;' 10 'i =2000:6000;' 10 'Data(1,i) = sin(f1*2*pi*t(i)) + 0.4 * cos(f2*2*pi*t(i));' 10 'Data = Data + 0.2 * sin(f3*2*pi*t) + 0.4 * rand(1,6000);']);

% Time-frequency options
TfOptions = struct(...
    'Comment',         'Power,1-60Hz', ...
    'TimeBands',       [], ...
    'Freqs',           [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60], ...
    'MorletFc',        1, ...
    'MorletFwhmTc',    3, ...
    'ClusterFuncTime', 'none', ...
    'Measure',         'power', ...
    'Output',          'average', ...
    'SaveKernel',       0);
% Process: Time-frequency (Morlet wavelets)
sSimTf1 = bst_process('CallProcess', 'process_timefreq', sSim, [], ...
    'edit',      TfOptions, ...
    'normalize', 'multiply');  % 1/f compensation: Multiply output values by frequency

% === NORMALIZATION ===
% Process: Time-frequency (Morlet wavelets)
sSimTf2 = bst_process('CallProcess', 'process_timefreq', sSim, [], ...
    'edit',      TfOptions, ...
    'normalize', 'none');  % None: Save non-standardized time-frequency maps
% Process: Spectral flattening
sSimTf2Multi = bst_process('CallProcess', 'process_tf_norm', sSimTf2, [], ...
    'normalize', 'multiply', ...  % 1/f compensation (multiple by frequency)
    'overwrite', 0);
% Process: Event-related perturbation (ERS/ERD): [750ms,1250ms]
sSimTf2Ersd = bst_process('CallProcess', 'process_baseline_norm', sSimTf2, [], ...
    'baseline',  [0.75, 1.25], ...
    'method',    'ersd', ...  % Event-related perturbation (ERS/ERD):    x_std = (x - μ) / μ * 100
    'overwrite', 0);

% Process: Snapshot: Time-frequency maps
bst_process('CallProcess', 'process_snapshot', sSimTf2, [], ...
    'target',   14, ...  % Time-frequency maps
    'Comment',  'Not normalized');
% Process: Snapshot: Time-frequency maps
bst_process('CallProcess', 'process_snapshot', sSimTf2Multi, [], ...
    'target',   14, ...  % Time-frequency maps
    'Comment',  'Spectral flattening: 1/f compensation');
% Process: Snapshot: Time-frequency maps
bst_process('CallProcess', 'process_snapshot', sSimTf2Ersd, [], ...
    'target',   14, ...  % Time-frequency maps
    'Comment',  'ERS/ERD');
% Spectrum/Time series
hFigTf1 = view_spectrum(sSimTf2.FileName, 'Spectrum');
hFigTf2 = view_spectrum(sSimTf2.FileName, 'TimeSeries');
panel_time('SetCurrentTime', 0.5);
panel_freq('SetCurrentFreq', 2, 0);
bst_report('Snapshot', [hFigTf1 hFigTf2], sSimTf2.FileName, 'Not normalized: 2s/20Hz', [200, 200, 400, 250]);
panel_time('SetCurrentTime', 2.02);
panel_freq('SetCurrentFreq', 20, 0);
bst_report('Snapshot', [hFigTf1 hFigTf2], sSimTf2.FileName, 'Not normalized: 2s/20Hz', [200, 200, 400, 250]);
bst_memory('UnloadAll', 'Forced');


% === HILBERT TRANSFORM ===
% Process: Hilbert transform
sSimHilbert = bst_process('CallProcess', 'process_hilbert', sSim, [], ...
    'edit', struct(...
         'Comment',         'Power', ...
         'TimeBands',       [], ...
         'Freqs',           {{'delta', '2, 4', 'mean'; 'theta', '5, 7', 'mean'; 'alpha', '8, 12', 'mean'; 'beta', '15, 29', 'mean'; 'gamma1', '30, 59', 'mean'; 'gamma2', '60, 90', 'mean'}}, ...
         'ClusterFuncTime', 'none', ...
         'Measure',         'power', ...
         'Output',          'all', ...
         'SaveKernel',      0), ...
    'normalize', 'none', ...  % None: Save non-standardized time-frequency maps
    'mirror',    0);
% Process: Spectral flattening
sSimHilbertMulti = bst_process('CallProcess', 'process_tf_norm', sSimHilbert, [], ...
    'normalize', 'multiply', ...  % 1/f compensation (multiple by frequency)
    'overwrite', 0);
% Process: Event-related perturbation (ERS/ERD): [750ms,1250ms]
sSimHilbertErsd = bst_process('CallProcess', 'process_baseline_norm', sSimHilbert, [], ...
    'baseline',  [0.75, 1.25], ...
    'method',    'ersd', ...  % Event-related perturbation (ERS/ERD):    x_std = (x - μ) / μ * 100
    'overwrite', 0);

% Process: Snapshot: Time-frequency maps
bst_process('CallProcess', 'process_snapshot', sSimHilbert, [], ...
    'target',   14, ...  % Time-frequency maps
    'Comment',  'Not normalized');
% Process: Snapshot: Time-frequency maps
bst_process('CallProcess', 'process_snapshot', sSimHilbertMulti, [], ...
    'target',   14, ...  % Time-frequency maps
    'Comment',  'Spectral flattening: 1/f compensation');
% Process: Snapshot: Time-frequency maps
bst_process('CallProcess', 'process_snapshot', sSimHilbertErsd, [], ...
    'target',   14, ...  % Time-frequency maps
    'Comment',  'ERS/ERD');

% === SINGLE TRIALS ===
TfOptions.Comment = 'Avg,Power,1-150Hz';
TfOptions.Freqs   = [1, 2, 3.1, 4.2, 5.4, 6.7, 8, 9.5, 11, 12.6, 14.3, 16.1, 18.1, 20.1, 22.3, 24.6, 27, 29.6, 32.4, 35.3, 38.4, 41.6, 45.1, 48.8, 52.7, 56.9, 61.3, 66, 70.9, 76.2, 81.8, 87.7, 94, 100.6, 107.7, 115.2, 123.1, 131.6, 140.5, 150];
% Process: Time-frequency (Morlet wavelets)
sEpochsAvgTf = bst_process('CallProcess', 'process_timefreq', sFilesEpochs1, [], ...
    'sensortypes', 'MEG, EEG', ...
    'edit',        TfOptions, ...
    'normalize',   'none');  % None: Save non-standardized time-frequency maps
% Process: Event-related perturbation (ERS/ERD): [-75ms,0ms]
sEpochsAvgTfErsd = bst_process('CallProcess', 'process_baseline_norm', sEpochsAvgTf, [], ...
    'baseline',  [-0.075, 0], ...
    'method',    'ersd', ...  % Event-related perturbation (ERS/ERD):    x_std = (x - μ) / μ * 100
    'overwrite', 0);

% === DISPLAY ===
% View time-frequency file
hFigTf1 = view_timefreq(sEpochsAvgTfErsd.FileName, 'SingleSensor');
% Configure display
sOptions = panel_display('GetDisplayOptions');
sOptions.HideEdgeEffects = 1;
sOptions.HighResolution = 1;
panel_display('SetDisplayOptions', sOptions);
% Other display modes
hFigTf2 = view_timefreq(sEpochsAvgTfErsd.FileName, 'AllSensors');
hFigTf3 = view_timefreq(sEpochsAvgTfErsd.FileName, '2DLayout');
hFigTf4 = view_timefreq(sEpochsAvgTfErsd.FileName, '2DLayoutOpt');
bst_colormaps('SetColormapName', 'stat2', 'jet');
bst_colormaps('SetColormapAbsolute', 'stat2', 1);
bst_report('Snapshot', hFigTf1, sEpochsAvgTfErsd.FileName, 'Time-frequency', [200, 200, 400, 250]);
bst_report('Snapshot', [hFigTf2 hFigTf3 hFigTf4], sEpochsAvgTfErsd.FileName, 'Time-frequency', [200, 200, 750, 400]);
close([hFigTf1 hFigTf2 hFigTf3 hFigTf4]);
% Image [channel x time]
hFigTf5 = view_erpimage(sEpochsAvgTfErsd.FileName, 'trialimage');
% Topographies
hFigTf6 = view_topography(sEpochsAvgTfErsd.FileName, 'MEG', '3DSensorCap');
hFigTf7 = view_topography(sEpochsAvgTfErsd.FileName, 'MEG', '2DDisc');
hFigTf8 = view_topography(sEpochsAvgTfErsd.FileName, 'MEG', '2DSensorCap');
hFigTf9 = view_topography(sEpochsAvgTfErsd.FileName, 'MEG', '2DLayout');
panel_time('SetCurrentTime', 0.175);
panel_freq('SetCurrentFreq', 8, 0);
bst_report('Snapshot', [hFigTf5 hFigTf6 hFigTf7 hFigTf8 hFigTf9], sEpochsAvgTfErsd.FileName, 'Time-frequency: 8Hz', [200, 200, 400, 250]);
close([hFigTf5 hFigTf6 hFigTf7 hFigTf8 hFigTf9]);


% === AVERAGE FOR SCOUTS ===
% Select all sources for the single deviant epochs
sFilesEpochDeviantSrc = bst_process('CallProcess', 'process_select_files_results', [], [], ...
    'subjectname', SubjectName, ...
    'condition',   '', ...
    'includebad',  0);
sFilesEpochDeviantSrc = bst_process('CallProcess', 'process_select_tag', sFilesEpochDeviantSrc, [], ...
    'tag',    'deviant', ...
    'search', 1, ...  % Search the file names
    'select', 1);     % Select only the files with the tag
sFilesEpochDeviantSrc = bst_process('CallProcess', 'process_select_tag', sFilesEpochDeviantSrc, [], ...
    'tag',    'average', ...
    'search', 1, ...  % Search the file names
    'select', 2);     % Exclude the files with the tag

% Process: Time-frequency (Morlet wavelets)
sFilesTfScout = bst_process('CallProcess', 'process_timefreq', sFilesEpochDeviantSrc, [], ...
    'clusters',   {'Destrieux', {'G_temp_sup-G_T_transv L', 'G_temp_sup-G_T_transv R', 'G_front_inf-Opercular L', 'G_precentral L'}}, ...
    'scoutfunc',  1, ...  % Mean
    'edit', struct(...
         'Comment',         'Deviant: Scouts,Avg,Power,1-150Hz', ...
         'TimeBands',       [], ...
         'Freqs',           [1, 2, 3.1, 4.2, 5.4, 6.7, 8, 9.5, 11, 12.6, 14.3, 16.1, 18.1, 20.1, 22.3, 24.6, 27, 29.6, 32.4, 35.3, 38.4, 41.6, 45.1, 48.8, 52.7, 56.9, 61.3, 66, 70.9, 76.2, 81.8, 87.7, 94, 100.6, 107.7, 115.2, 123.1, 131.6, 140.5, 150], ...
         'MorletFc',        1, ...
         'MorletFwhmTc',    3, ...
         'ClusterFuncTime', 'after', ...
         'Measure',         'power', ...
         'Output',          'average', ...
         'SaveKernel',      0), ...
    'normalize',  'none');   % None: Save non-standardized time-frequency maps)
% Process: Event-related perturbation (ERS/ERD): [-75ms,0ms]
sFilesTfScoutErsd = bst_process('CallProcess', 'process_baseline_norm', sFilesTfScout, [], ...
    'baseline',  [-0.075, 0], ...
    'method',    'ersd', ...  % Event-related perturbation (ERS/ERD):    x_std = (x - μ) / μ * 100
    'overwrite', 0);
% Process: Snapshot: Time-frequency maps
bst_process('CallProcess', 'process_snapshot', sFilesTfScoutErsd, [], ...
    'target',   14, ...  % Time-frequency maps
    'Comment',  'ERS/ERD');


% === FULL CORTEX / HILBERT ===
% Process: Hilbert transform
sFilesHilbertCortex = bst_process('CallProcess', 'process_hilbert', sFilesEpochDeviantSrc, [], ...
    'clusters',  {}, ...
    'scoutfunc', 1, ...  % Mean
    'edit',      struct(...
         'Comment',         'Deviant: Avg,Magnitude', ...
         'TimeBands',       [], ...
         'Freqs',           {{'delta', '2, 4', 'mean'; 'theta', '5, 7', 'mean'; 'alpha', '8, 12', 'mean'; 'beta', '15, 29', 'mean'; 'gamma1', '30, 59', 'mean'; 'gamma2', '60, 90', 'mean'}}, ...
         'ClusterFuncTime', 'none', ...
         'Measure',         'power', ...
         'Output',          'average', ...
         'RemoveEvoked',    0, ...
         'SaveKernel',      0), ...
    'normalize', 'none', ...  % None: Save non-standardized time-frequency maps
    'mirror',    0);
% Process: Event-related perturbation (ERS/ERD): [-75ms,0ms]
sFilesHilbertCortexErsd = bst_process('CallProcess', 'process_baseline_norm', sFilesHilbertCortex, [], ...
    'baseline',  [-0.075, 0], ...
    'method',    'ersd', ...  % Event-related perturbation (ERS/ERD):    x_std = (x - μ) / μ * 100
    'overwrite', 0);

% View results
hFigTf1 = view_surface_data([], sFilesHilbertCortexErsd.FileName);
hFigTf2 = view_timefreq(sFilesHilbertCortexErsd.FileName, 'SingleSensor', 362);
figure_3d('SetStandardView', hFigTf1, 'left');
panel_surface('SetDataThreshold', hFigTf1, 1, 0.5);
panel_time('SetCurrentTime', 0.175);
panel_freq('SetCurrentFreq', 3);
bst_colormaps('RestoreDefaults', 'stat2');
bst_report('Snapshot', [hFigTf1 hFigTf2], sFilesHilbertCortexErsd.FileName, 'Hilbert transform: Alpha band', [200, 200, 400, 250]);
bst_memory('UnloadAll', 'Forced');


%% ===== TUTORIAL #25: DIFFRERENCE ===================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #25: Difference' 10]);

% ===== SELECT TRIALS (DATA) =====
% Process: Select recordings in: Subject01/*
sFilesAll = bst_process('CallProcess', 'process_select_files_data', [], [], ...
    'subjectname', SubjectName, ...
    'condition',   '', ...
    'includebad',  0);
% Process: Select file names with tag: deviant_trial
sEpochDeviant = bst_process('CallProcess', 'process_select_tag', sFilesAll, [], ...
    'tag',    'deviant_trial', ...
    'search', 1, ...  % Search the file names
    'select', 1);     % Select only the files with the tag
% Process: Select file names with tag: standard_trial
sEpochStandard = bst_process('CallProcess', 'process_select_tag', sFilesAll, [], ...
    'tag',    'standard_trial', ...
    'search', 1, ...  % Search the file names
    'select', 1);     % Select only the files with the tag

% ===== SELECT TRIALS (SOURCE) =====
% Process: Select recordings in: Subject01/*
sFilesAllSrc = bst_process('CallProcess', 'process_select_files_results', [], [], ...
    'subjectname', SubjectName, ...
    'condition',   '', ...
    'includebad',  0);
% Process: Select file names with tag: deviant_trial
sEpochDeviantSrc = bst_process('CallProcess', 'process_select_tag', sFilesAllSrc, [], ...
    'tag',    'deviant_trial', ...
    'search', 1, ...  % Search the file names
    'select', 1);     % Select only the files with the tag
% Process: Select file names with tag: standard_trial
sEpochStandardSrc = bst_process('CallProcess', 'process_select_tag', sFilesAllSrc, [], ...
    'tag',    'standard_trial', ...
    'search', 1, ...  % Search the file names
    'select', 1);     % Select only the files with the tag

% ===== ABSOLUTE DIFFERENCE ======
% Process: Difference: A-B, abs
sDiffSrc = bst_process('CallProcess', 'process_diff_ab', sFilesIntraSrc(1).FileName, sFilesIntraSrc(2).FileName, ...
    'source_abs', 1);
% Process: Set comment: deviant|abs - standard|abs
sDiffSrc = bst_process('CallProcess', 'process_set_comment', sDiffSrc, [], ...
    'tag',     'deviant|abs - standard|abs', ...
    'isindex', 1);
% Process: Low-pass:40Hz
sDiffSrcZscore = bst_process('CallProcess', 'process_bandpass', sDiffSrc, [], ...
    'highpass',    0, ...
    'lowpass',     40, ...
    'attenuation', 'strict', ...  % 60dB
    'mirror',      0, ...
    'overwrite',   1);
% Process: Z-score transformation: [-100ms,-2ms]
sDiffSrcZscore = bst_process('CallProcess', 'process_baseline_norm', sDiffSrcZscore, [], ...
    'baseline',   [-0.1, -0.002], ...
    'source_abs', 0, ...
    'method',     'zscore', ...  % Z-score transformation:    x_std = (x - μ) / σ
    'overwrite',  0);
% Process: Snapshot: Sources (contact sheet)
bst_process('CallProcess', 'process_snapshot', sDiffSrcZscore, [], ...
    'target',         9, ...  % Sources (contact sheet)
    'modality',       1, ...  % MEG (All)
    'orient',         1, ...  % left
    'contact_time',   [0, 0.35], ...
    'contact_nimage', 15, ...
    'threshold',      30, ...
    'Comment',        'Difference deviant - standard (absolute)');

% ===== RELATIVE DIFFERENCE =====
% Process: Difference: A-B
sDiffSrcRel = bst_process('CallProcess', 'process_diff_ab', sFilesIntraSrc(1).FileName, sFilesIntraSrc(2).FileName, ...
    'source_abs', 0);
% Process: Set comment: deviant - standard
sDiffSrcRel = bst_process('CallProcess', 'process_set_comment', sDiffSrcRel, [], ...
    'tag',     'deviant - standard', ...
    'isindex', 1);
% Process: Low-pass:40Hz
sDiffSrcRelZscore = bst_process('CallProcess', 'process_bandpass', sDiffSrcRel, [], ...
    'highpass',    0, ...
    'lowpass',     40, ...
    'attenuation', 'strict', ...  % 60dB
    'mirror',      0, ...
    'overwrite',   1);
% Process: Z-score transformation: [-100ms,-2ms]
sDiffSrcRelZscore = bst_process('CallProcess', 'process_baseline_norm', sDiffSrcRelZscore, [], ...
    'baseline',   [-0.1, -0.002], ...
    'source_abs', 0, ...
    'method',     'zscore', ...  % Z-score transformation:    x_std = (x - μ) / σ
    'overwrite',  0);
% Configure colormap: hot/absolute
bst_colormaps('SetColormapName', 'stat2', 'hot');
bst_colormaps('SetColormapAbsolute', 'stat2', 1);
% Process: Snapshot: Sources (contact sheet)
bst_process('CallProcess', 'process_snapshot', sDiffSrcRelZscore, [], ...
    'target',         9, ...  % Sources (contact sheet)
    'modality',       1, ...  % MEG (All)
    'orient',         1, ...  % left
    'contact_time',   [0, 0.35], ...
    'contact_nimage', 15, ...
    'threshold',      30, ...
    'Comment',        'Difference deviant - standard (relative)');
% Restore colormap: rwb/relative
bst_colormaps('SetColormapName', 'stat2', 'cmap_rbw');
bst_colormaps('SetColormapAbsolute', 'stat2', 0);

% ===== DIFFERENCE OF MEANS =====
% Process: Select uniform number of files  [uniform]
[sEpochDeviantUni, sEpochStandardUni] = bst_process('CallProcess', 'process_select_uniform2', sEpochDeviant, sEpochStandard, ...
    'nfiles', 0, ...
    'method', 4);  % Uniformly distributed
% Process: Difference of means [mean]
sDiffMean = bst_process('CallProcess', 'process_diff_mean', sEpochDeviantUni, sEpochStandardUni, ...
    'avg_func', 1, ...  % Arithmetic average mean(A) - mean(B)
    'weighted', 0);
% Process: Snapshot: Recordings time series
bst_process('CallProcess', 'process_snapshot', sDiffMean, [], ...
    'target',     5, ...  % Recordings time series
    'modality',   1, ...  % MEG (All)
    'Comment',    'Difference of means');



%% ===== TUTORIAL #26: STATISTICS ====================================================
%  ===================================================================================
disp([10 'DEMO> Tutorial #26: Statistics' 10]);
% ===== HISTOGRAMS =====
% Process: Extract values: [160ms] MLP57
sHistoDeviant = bst_process('CallProcess', 'process_extract_values', sEpochDeviant, [], ...
    'timewindow',  [0.16, 0.16], ...
    'sensortypes', 'MLP57', ...
    'isabs',       0, ...
    'avgtime',     0, ...
    'avgrow',      0, ...
    'dim',         2, ...  % Concatenate time (dimension 2)
    'Comment',     '');
% Process: Extract values: [160ms] MLP57
sHistoStandard = bst_process('CallProcess', 'process_extract_values', sEpochStandard, [], ...
    'timewindow',  [0.16, 0.16], ...
    'sensortypes', 'MLP57', ...
    'isabs',       0, ...
    'avgtime',     0, ...
    'avgrow',      0, ...
    'dim',         2, ...  % Concatenate time (dimension 2)
    'Comment',     '');
% Display histograms
hFigHisto = view_histogram({sHistoDeviant.FileName, sHistoStandard.FileName});
bst_report('Snapshot', hFigHisto, sHistoDeviant.FileName, 'Histograms for MLP57/160ms');
close(hFigHisto);

% ===== EXEMPLE #1: PARAMETRIC/DATA =====
% Process: t-test [equal] [-100ms,500ms]          H0:(A-B = 0)
sTestParamData = bst_process('CallProcess', 'process_test_parametric2', sEpochDeviant, sEpochStandard, ...
    'timewindow',    [-0.1, 0.5], ...
    'sensortypes',   '', ...
    'isabs',         0, ...
    'avgtime',       0, ...
    'avgrow',        0, ...
    'Comment',       '', ...
    'test_type',     'ttest_equal', ...  % Student's t-test   (equal variance) t = (mean(A)-mean(B)) / (Sx * sqrt(1/nA + 1/nB))Sx = sqrt(((nA-1)*var(A) + (nB-1)*var(B)) / (nA+nB-2)) df = nA + nB - 2
    'tail',          'two');  % Two-tailed
% Set display properties
StatThreshOptions = bst_get('StatThreshOptions');
StatThreshOptions.pThreshold = 0.05;
StatThreshOptions.Correction = 'fdr';
StatThreshOptions.Control    = [1 2 3];
bst_set('StatThreshOptions', StatThreshOptions);
% Process: Snapshot: Recordings time series
bst_process('CallProcess', 'process_snapshot', sTestParamData, [], ...
    'target',     5, ...  % Recordings time series
    'modality',   1, ...  % MEG (All)
    'time',       0.16, ...
    'Comment',    'Parametric t-test (p<0.05, FDR)');
% Process: Snapshot: Recordings topography (one time)
bst_process('CallProcess', 'process_snapshot', sTestParamData, [], ...
    'target',         6, ...  % Recordings topography (one time)
    'modality',       1, ...  % MEG (All)
    'time',           0.16, ...
    'Comment',        'Parametric t-test (p<0.05, FDR)');

% ===== EXEMPLE #2: NON-PARAMETRIC/DATA =====
% Process: Perm t-test equal [-100ms,500ms MEG]          H0:(A=B), H1:(A<>B)
sTestPermData = bst_process('CallProcess', 'process_test_permutation2', sEpochDeviant, sEpochStandard, ...
    'timewindow',     [-0.1, 0.5], ...
    'sensortypes',    'MEG', ...
    'isabs',          0, ...
    'avgtime',        0, ...
    'avgrow',         0, ...
    'iszerobad',      1, ...
    'Comment',        '', ...
    'test_type',      'ttest_equal', ...  % Student's t-test   (equal variance) t = (mean(A)-mean(B)) / (Sx * sqrt(1/nA + 1/nB))Sx = sqrt(((nA-1)*var(A) + (nB-1)*var(B)) / (nA+nB-2))
    'randomizations', 1000, ...
    'tail',           'two');  % Two-tailed
% Process: Snapshot: Recordings time series
bst_process('CallProcess', 'process_snapshot', sTestPermData, [], ...
    'target',     5, ...  % Recordings time series
    'modality',   1, ...  % MEG (All)
    'time',       0.16, ...
    'Comment',    'Non-parametric t-test (p<0.05, FDR)');
% Process: Snapshot: Recordings topography (one time)
bst_process('CallProcess', 'process_snapshot', sTestPermData, [], ...
    'target',         6, ...  % Recordings topography (one time)
    'modality',       1, ...  % MEG (All)
    'time',           0.16, ...
    'Comment',        'Non-parametric t-test (p<0.05, FDR)');

% ===== EXEMPLE #3: CLUSTER/DATA =====
% Process: FT t-test unequal cluster [-100ms,500ms MEG]          H0:(A=B), H1:(A<>B)
sTestClustData = bst_process('CallProcess', 'process_ft_timelockstatistics', sEpochDeviant, sEpochStandard, ...
    'sensortypes',    'MEG', ...
    'timewindow',     [-0.1, 0.5], ...
    'isabs',          0, ...
    'avgtime',        0, ...
    'avgchan',        0, ...
    'randomizations', 1000, ...
    'statistictype',  1, ...      % Independent t-test
    'tail',           'two', ...  % Two-tailed
    'correctiontype', 2, ...      % cluster
    'minnbchan',      0, ...
    'clusteralpha',   0.05);
% Process: Snapshot: Recordings time series
bst_process('CallProcess', 'process_snapshot', sTestClustData, [], ...
    'target',    5, ...  % Recordings time series
    'time',      0.16, ...
    'modality',  1, ...  % MEG (All)
    'Comment',   'Cluster-based permutation test');
% Process: Snapshot: Recordings topography (one time)
bst_process('CallProcess', 'process_snapshot', sTestClustData, [], ...
    'target',    6, ...  % Recordings topography (one time)
    'modality',  1, ...  % MEG (All)
    'time',      0.16, ...
    'Comment',   'Cluster-based permutation test');

% ===== EXAMPLE #4: PARAMETRIC/SOURCES =====
% Process: t-test [equal] [-100ms,500ms]          H0:(A-B = 0)
sTestParamSrc = bst_process('CallProcess', 'process_test_parametric2', sEpochDeviantSrc, sEpochStandardSrc, ...
    'timewindow',    [-0.1, 0.5], ...
    'scoutsel',      {}, ...
    'scoutfunc',     1, ...  % Mean
    'isnorm',        0, ...
    'avgtime',       0, ...
    'Comment',       '', ...
    'test_type',     'ttest_equal', ...  % Student's t-test   (equal variance) t = (mean(A)-mean(B)) / (Sx * sqrt(1/nA + 1/nB))Sx = sqrt(((nA-1)*var(A) + (nB-1)*var(B)) / (nA+nB-2)) df = nA + nB - 2
    'tail',          'two');  % Two-tailed
% Process: Difference of means [abs(mean)]
sDiffMeanSrc = bst_process('CallProcess', 'process_diff_mean', sEpochDeviantSrc, sEpochStandardSrc, ...
    'avg_func',   2, ...  % Absolute value of average abs(mean(A)) - abs(mean(B))
    'weighted',   0);
% Process: Apply statistic threshold: p<0.05 (FDR:1,2,3)
sDiffMeanSrcThresh = bst_process('CallProcess', 'process_extract_pthresh2', sTestParamSrc, sDiffMeanSrc, ...
    'pthresh',    0.05, ...
    'correction', 3, ...  % False discovery rate (FDR)
    'control1',   1, ...
    'control2',   1, ...
    'control3',   1);
% Process: Snapshot: Sources (one time)
bst_process('CallProcess', 'process_snapshot', sTestParamSrc, [], ...
    'target',    8, ...  % Sources (one time)
    'orient',    1, ...  % left
    'time',      0.148, ...
    'threshold', 40, ...
    'Comment',   'Parametric t-test (p<0.05, FDR)');
% Process: Snapshot: Sources (one time)
bst_process('CallProcess', 'process_snapshot', sDiffMeanSrc, [], ...
    'target',    8, ...  % Sources (one time)
    'orient',    1, ...  % left
    'time',      0.148, ...
    'threshold', 40, ...
    'Comment',   'abs(average(deviant)) - abs(average(standard))');
% Process: Snapshot: Sources (one time)
bst_process('CallProcess', 'process_snapshot', sDiffMeanSrcThresh, [], ...
    'target',    8, ...  % Sources (one time)
    'orient',    1, ...  % left
    'time',      0.148, ...
    'threshold', 0, ...
    'Comment',   'Different of mean thresholded with t-test results');

% ===== EXAMPLE #5: PARAMETRIC/SCOUTS =====
% Process: t-test equal [-100ms,500ms]          H0:(A=B), H1:(A<>B)
sTestParamScout = bst_process('CallProcess', 'process_test_parametric2', sEpochDeviantSrc, sEpochStandardSrc, ...
    'timewindow',    [-0.1, 0.5], ...
    'scoutsel',      {'Destrieux', {'G_front_inf-Opercular L', 'G_precentral L', 'G_temp_sup-G_T_transv L'}}, ...
    'scoutfunc',     1, ...  % Mean
    'isnorm',        0, ...
    'avgtime',       0, ...
    'Comment',       '', ...
    'test_type',     'ttest_equal', ...  % Student's t-test   (equal variance) t = (mean(A)-mean(B)) / (Sx * sqrt(1/nA + 1/nB))Sx = sqrt(((nA-1)*var(A) + (nB-1)*var(B)) / (nA+nB-2)) df = nA + nB - 2
    'tail',          'two');  % Two-tailed
% Process: Apply statistic threshold: p<0.05 (FDR:1,2,3)
sTestParamScoutThresh = bst_process('CallProcess', 'process_extract_pthresh', sTestParamScout, [], ...
    'pthresh',    0.05, ...
    'correction', 3, ...  % False discovery rate (FDR)
    'control1',   1, ...
    'control2',   1, ...
    'control3',   1);
% Process: Compute head model
bst_process('CallProcess', 'process_headmodel', sTestParamScoutThresh, [], ...
    'sourcespace', 1, ...  % Cortex surface
    'meg',         3);     % Overlapping spheres
% Process: Simulate recordings from scouts
sSimulData = bst_process('CallProcess', 'process_simulate_recordings', sTestParamScoutThresh, [], ...
    'scouts',      {'Destrieux', {'G_front_inf-Opercular L', 'G_precentral L', 'G_temp_sup-G_T_transv L'}}, ...
    'savesources', 1);

% Get corresponding source file
[sStudy,iStudy,iRes] = bst_get('ResultsForDataFile', sSimulData.FileName);
sSimulSrc = sStudy.Result(iRes).FileName;
% Reset visualization filters
panel_filter('SetFilters', 0, [], 0, [], 0, [], 0, 0);
% Process: Snapshot: Recordings time series
bst_process('CallProcess', 'process_snapshot', sTestParamScout, [], ...
    'target',    5, ...  % Recordings time series
    'time',      0.148, ...
    'Comment',   'Parametric t-test (p<0.05, FDR)');
% Process: Snapshot: Sources (one time)
bst_process('CallProcess', 'process_snapshot', sSimulSrc, [], ...
    'target',    8, ...  % Sources (one time)
    'orient',    1, ...  % left
    'time',      0.148, ...
    'threshold', 0, ...
    'Comment',   'Simulated sources');
% Process: Snapshot: Recordings time series
bst_process('CallProcess', 'process_snapshot', sSimulData, [], ...
    'target',    5, ...  % Recordings time series
    'modality',  1, ...  % MEG (All)
    'time',      0.148, ...
    'Comment',   'Simulated MEG recordings');


% ===== EXAMPLE #6: NON-PARAMETRIC/TIMEFREQ =====
TfOptions.Output = 'all';
% Process: Time-frequency (Morlet wavelets) / DEVIANT
sEpochDeviantTf = bst_process('CallProcess', 'process_timefreq', sEpochDeviant, [], ...
    'sensortypes', 'MLP57', ...
    'edit',        TfOptions, ...
    'normalize',   'none');  % None: Save non-standardized time-frequency maps
% Process: Time-frequency (Morlet wavelets) / STANDARD
sEpochStandardTf = bst_process('CallProcess', 'process_timefreq', sEpochStandard, [], ...
    'sensortypes', 'MLP57', ...
    'edit',        TfOptions, ...
    'normalize',   'none');  % None: Save non-standardized time-frequency maps
% Process: Perm t-test equal [-100ms,500ms 1-150Hz]          H0:(A=B), H1:(A<>B)
sTestTf = bst_process('CallProcess', 'process_test_permutation2', sEpochDeviantTf, sEpochStandardTf, ...
    'timewindow',     [-0.1, 0.5], ...
    'freqrange',      [1, 150], ...
    'rows',           '', ...
    'isabs',          0, ...
    'avgtime',        0, ...
    'avgrow',         0, ...
    'avgfreq',        0, ...
    'matchrows',      0, ...
    'iszerobad',      1, ...
    'Comment',        '', ...
    'test_type',      'ttest_equal', ...  % Student's t-test   (equal variance) t = (mean(A)-mean(B)) / (Sx * sqrt(1/nA + 1/nB))Sx = sqrt(((nA-1)*var(A) + (nB-1)*var(B)) / (nA+nB-2))
    'randomizations', 1000, ...
    'tail',           'two');  % Two-tailed
% Set stat threshold
StatThreshOptions.pThreshold = 0.05;
StatThreshOptions.Correction = 'none';
bst_set('StatThreshOptions', StatThreshOptions);
% Process: Snapshot: Time-frequency maps
bst_process('CallProcess', 'process_snapshot', sTestTf, [], ...
    'target',   14, ...  % Time-frequency maps
    'Comment',  'Non-parametric t-test (p<0.05, Uncorrected)');
% Process: Delete intermediate results
bst_process('CallProcess', 'process_delete', [sEpochDeviantTf, sEpochStandardTf], [], ...
    'target', 1);  % Delete selected files



%% ===== SAVE REPORT =====
% Save and display report
ReportFile = bst_report('Save', []);
if ~isempty(reports_dir) && ~isempty(ReportFile)
    bst_report('Export', ReportFile, reports_dir);
else
    bst_report('Open', ReportFile);
end

disp([10 'DEMO> Done.' 10]);

For an example of a script illustrating how to create loops, look at the tutorial MEG visual: single subject. brainstorm3/toolbox/script/tutorial_visual_single.m - Report: report_TutorialVisual_sub001.html

function tutorial_visual_single(bids_dir, reports_dir)
% TUTORIAL_VISUAL_SINGLE: Runs the Brainstorm/SPM group analysis pipeline (single subject, BIDS version).
%
% ONLINE TUTORIALS: https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle
%
% INPUTS:
%    - bids_dir: Path to folder ds000117 (https://openneuro.org/datasets/ds000117)
%       |- derivatives/freesurfer/sub-XX                               : Segmentation folders generated with FreeSurfer
%       |- derivatives/meg_derivatives/sub-XX/ses-meg/meg/*.fif        : MEG+EEG recordings (processed with MaxFilter's SSS)
%       |- derivatives/meg_derivatives/sub-emptyroom/ses-meg/meg/*.fif : Empty room measurements
%    - reports_dir: If defined, exports all the reports as HTML to this folder

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
% 
% Copyright (c)2000-2020 University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
% 
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
%
% For more information type "brainstorm license" at command prompt.
% =============================================================================@
%
% Author: Francois Tadel, Elizabeth Bock, 2016-2018


%% ===== SCRIPT VARIABLES =====
% Full list of subjects to process
SubjectNames = {'sub-01', 'sub-02', 'sub-03', 'sub-04', 'sub-05', 'sub-06', 'sub-07', 'sub-08', ...
                'sub-09', 'sub-10', 'sub-11', 'sub-12', 'sub-13', 'sub-14', 'sub-15', 'sub-16'};
% Empty-room dates for each subject (so that we can match automatically recordings with empty-room)
EmptyRoomSubj = 'sub-emptyroom';
AcquisitionDates = {'09-Apr-2009', '06-May-2009', '11-May-2009', '18-May-2009', '15-May-2009', '15-May-2009', '15-May-2009', '15-May-2009', ...
                    '15-May-2009', '15-May-2009', '01-Jun-2009', '01-Jun-2009', '01-Jun-2009', '26-Nov-2009', '08-Dec-2009', '08-Dec-2009'};
% Bad channels {iSubj} = {Run01, Run02, Run03, Run04, Run05, Run06}
BadChannels{1}  = {'EEG016', 'EEG070', 'EEG050',{'EEG008','EEG050'}, [], []};
BadChannels{2}  = {{'EEG027', 'EEG030', 'EEG038'}, 'EEG010', 'EEG010', 'EEG010', 'EEG010', 'EEG010'};
BadChannels{3}  = {{'EEG008','EEG017'}, {'EEG008','EEG017'}, {'EEG008','EEG017'}, {'EEG008','EEG017'}, {'EEG008','EEG017','EEG001'}, {'EEG008','EEG017','EEG020'}};
BadChannels{4}  = {{'EEG038'}, {'EEG038','EEG001','EEG016'}, {'EEG038','EEG001','EEG016'}, {'EEG038','EEG001'}, {'EEG038','EEG001','EEG016'}, {'EEG038','EEG001','EEG016'}};
BadChannels{5}  = {'EEG001', 'EEG001', [], [], [], []};
BadChannels{6}  = {'EEG068', [], 'EEG004', [], [], []};
BadChannels{7}  = {[], [], {'EEG004','EEG008'}, {'EEG004','EEG008'},{'EEG004','EEG008','EEG043','EEG045','EEG047'}, {'EEG004','EEG008'}};
BadChannels{8}  = {[], [], [], [], [], []};
BadChannels{9}  = {[], 'EEG004', 'EEG004', [], 'EEG004', 'EEG004'};
BadChannels{10} = {[], [], [], [], [], []};
BadChannels{11} = {{'EEG010','EEG050'}, 'EEG050', 'EEG050', 'EEG050', 'EEG050', 'EEG050'};
BadChannels{12} = {{'EEG024','EEG057'}, {'EEG024','EEG057'}, {'EEG024','EEG057'}, {'EEG024','EEG057','EEG070'}, {'EEG024','EEG057'}, {'EEG024','EEG057','EEG070'}};
BadChannels{13} = {'EEG009', 'EEG009', {'EEG009','EEG057','EEG69'}, 'EEG009', {'EEG009','EEG044'}, {'EEG009','EEG044'}};
BadChannels{14} = {'EEG029', 'EEG029', 'EEG029', {'EEG004','EEG008','EEG016','EEG029'}, {'EEG004','EEG008','EEG016','EEG029'}, {'EEG004','EEG008','EEG016','EEG029'}};
BadChannels{15} = {'EEG038', 'EEG038', 'EEG038', 'EEG038', {'EEG054','EEG038'}, 'EEG038'};
BadChannels{16} = {'EEG008', 'EEG008', 'EEG008', 'EEG008', 'EEG008', 'EEG008'};
% SSP components to remove {iSubj} = {sRun01, sRun02, sRun03, sRun03, sRun04, sRun05, sRun06},   sRun0X={ECG_GRAD,ECG_MAG}
SspSelect{1}  = {{1,1},         {1,1},   {1,1},   {1,1},   {1,1},   {1,1}}; 
SspSelect{2}  = {{1,1},         {1,1},   {1,1},   {1,1},   {3,1},   {1,1}};
SspSelect{3}  = {{[],1},        {1,1},   {1,1},   {1,1},   {1,1},   {1,1}};
SspSelect{4}  = {{[],1},        {[],1},  {[],1},  {[],1},  {[],1},  {[],1}};
SspSelect{5}  = {{2,1},         {1,1},   {1,1},   {[],1},  {1,1},   {1,1}};
SspSelect{6}  = {{2,1},         {2,1},   {1,1},   {2,1},   {1,1},   {2,1}};
SspSelect{7}  = {{1,1},         {1,1},   {1,1},   {1,1},   {1,1},   {1,1}};
SspSelect{8}  = {{1,1},         {1,1},   {[],1},  {2,1},   {1,1},   {2,1}};
SspSelect{9}  = {{1,1},         {1,1},   {[],1},  {[],1},  {1,1},   {1,1}};
SspSelect{10} = {{1,1},         {1,1},   {1,1},   {1,1},   {1,1},   {1,1}};
SspSelect{11} = {{[],1},        {[],1},  {[],1},  {[],1},  {[],[]}, {[],[]}};
SspSelect{12} = {{[1,2],[1,2]}, {1,1},   {1,1},   {1,1},   {1,1},   {1,1}};
SspSelect{13} = {{[],[]},       {[],[]}, {[],[]}, {[],[]}, {[],[]}, {[],[]}};
SspSelect{14} = {{1,1},         {1,1},   {1,1},   {1,1},   {1,1},   {1,1}};
SspSelect{15} = {{1,1},         {1,1},   {1,1},   {1,1},   {1,1},   {1,1}};
SspSelect{16} = {{1,1},         {1,1},   {1,1},   {2,1},   {1,1},   {1,1}};


%% ===== CREATE PROTOCOL =====
% Start brainstorm without the GUI
if ~brainstorm('status')
    brainstorm nogui
end
% Output folder for reports
if (nargin < 2) || isempty(reports_dir) || ~isdir(reports_dir)
    reports_dir = [];
end
% You have to specify the folder in which the tutorial dataset is unzipped
if (nargin < 1) || isempty(bids_dir) || ~file_exist(bids_dir) || ~file_exist(bst_fullfile(bids_dir, 'derivatives')) || ~file_exist(bst_fullfile(bids_dir, 'dataset_description.json'))
    error('The first argument must be the full path to the tutorial folder.');
end
% The protocol name has to be a valid folder name (no spaces, no weird characters...)
ProtocolName = 'TutorialVisual';
% Delete existing protocol
gui_brainstorm('DeleteProtocol', ProtocolName);
% Create new protocol
gui_brainstorm('CreateProtocol', ProtocolName, 0, 0);
% Set visualization filters: 40Hz low-pass, no high-pass
panel_filter('SetFilters', 1, 40, 0, [], 0, [], 0, 0);
% Set colormap: local color scale
bst_colormaps('SetMaxMode', 'meg', 'local');
bst_colormaps('SetMaxMode', 'eeg', 'local');


%% ===== PRE-PROCESS AND IMPORT =====
for iSubj = 1:16
    % Start a new report (one report per subject)
    bst_report('Start');
    disp(sprintf('\n===== IMPORT: SUBJECT #%d =====\n', iSubj));
    
    % If subject already exists: delete it
    [sSubject, iSubject] = bst_get('Subject', SubjectNames{iSubj});
    if ~isempty(sSubject)
        db_delete_subjects(iSubject);
    end
    
    % ===== FILES TO IMPORT =====
    % Build the path of the files to import
    AnatDir    = fullfile(bids_dir, 'derivatives', 'freesurfer', SubjectNames{iSubj}, 'ses-mri', 'anat');
    DataDir    = fullfile(bids_dir, 'derivatives',  'meg_derivatives', SubjectNames{iSubj}, 'ses-meg', 'meg');
    % Check if the folder contains the required files
    if ~file_exist(AnatDir)
        error(['The folder "' AnatDir '" does not exist.']);
    end
    if ~file_exist(DataDir)
        error(['The folder "' DataDir '" does not exist.']);
    end

    % ===== ANATOMY =====
    % Process: Import anatomy folder
    bst_process('CallProcess', 'process_import_anatomy', [], [], ...
        'subjectname', SubjectNames{iSubj}, ...
        'mrifile',     {AnatDir, 'FreeSurfer'}, ...
        'nvertices',   15000);
    
    % ===== PROCESS EACH RUN =====
    for iRun = 1:6
        % Files to import
        FifFile = bst_fullfile(DataDir, sprintf('%s_ses-meg_task-facerecognition_run-%02d_proc-sss_meg.fif', SubjectNames{iSubj}, iRun));

        % ===== LINK CONTINUOUS FILE =====
        % Process: Create link to raw file
        sFileRaw = bst_process('CallProcess', 'process_import_data_raw', [], [], ...
            'subjectname',    SubjectNames{iSubj}, ...
            'datafile',       {FifFile, 'FIF'}, ...
            'channelreplace', 1, ...
            'channelalign',   0);
        % Set acquisition date
        panel_record('SetAcquisitionDate', sFileRaw.iStudy, AcquisitionDates{iSubj});

        % ===== PREPARE CHANNEL FILE =====
        % Process: Set channels type
        bst_process('CallProcess', 'process_channel_settype', sFileRaw, [], ...
            'sensortypes', 'EEG061, EEG064', ...
            'newtype',     'NOSIG');
        bst_process('CallProcess', 'process_channel_settype', sFileRaw, [], ...
            'sensortypes', 'EEG062', ...
            'newtype',     'EOG');
        bst_process('CallProcess', 'process_channel_settype', sFileRaw, [], ...
            'sensortypes', 'EEG063', ...
            'newtype',     'ECG');

        % Process: Remove head points
        sFileRaw = bst_process('CallProcess', 'process_headpoints_remove', sFileRaw, [], ...
            'zlimit', 0);
        % Process: Refine registration
        sFileRaw = bst_process('CallProcess', 'process_headpoints_refine', sFileRaw, []);
        % Process: Project electrodes on scalp
        sFileRaw = bst_process('CallProcess', 'process_channel_project', sFileRaw, []);

        % Process: Snapshot: Sensors/MRI registration
        bst_process('CallProcess', 'process_snapshot', sFileRaw, [], ...
            'target',   1, ...  % Sensors/MRI registration
            'modality', 1, ...  % MEG (All)
            'orient',   1, ...  % left
            'Comment',  sprintf('MEG/MRI Registration: Subject #%d, Run #%d', iSubj, iRun));
        bst_process('CallProcess', 'process_snapshot', sFileRaw, [], ...
            'target',   1, ...  % Sensors/MRI registration
            'modality', 4, ...  % EEG
            'orient',   1, ...  % left
            'Comment',  sprintf('EEG/MRI Registration: Subject #%d, Run #%d', iSubj, iRun));

        % ===== IMPORT TRIGGERS =====
        % Process: Read from channel
        bst_process('CallProcess', 'process_evt_read', sFileRaw, [], ...
            'stimchan',  'STI101', ...
            'trackmode', 2, ...  % Bit: detect the changes for each bit independently
            'zero',      0);
        % Process: Group by name
        bst_process('CallProcess', 'process_evt_groupname', sFileRaw, [], ...
            'combine', 'Unfamiliar=3,4', ...
            'dt',      0, ...
            'delete',  1);
        % Process: Rename event
        bst_process('CallProcess', 'process_evt_rename', sFileRaw, [], ...
            'src',  '3', ...
            'dest', 'Famous');
        % Process: Rename event
        bst_process('CallProcess', 'process_evt_rename', sFileRaw, [], ...
            'src',  '5', ...
            'dest', 'Scrambled');
        % Process: Add time offset
        bst_process('CallProcess', 'process_evt_timeoffset', sFileRaw, [], ...
            'info',      [], ...
            'eventname', 'Famous, Unfamiliar, Scrambled', ...
            'offset',    0.0345);
        % Process: Delete events
        bst_process('CallProcess', 'process_evt_delete', sFileRaw, [], ...
            'eventname', '1,2,6,7,8,9,10,11,12,13,14,15,16');
        % Process: Detect cHPI activity (Elekta):STI201
        bst_process('CallProcess', 'process_evt_detect_chpi', sFileRaw, [], ...
            'eventname',   'chpi_bad', ...
            'channelname', 'STI201', ...
            'method',      'off');  % Mark as bad when the HPI coils are OFF
        
        % ===== FREQUENCY FILTERS =====
        % Process: Notch filter: 50Hz 100Hz 150Hz 200Hz
        sFileClean = bst_process('CallProcess', 'process_notch', sFileRaw, [], ...
            'freqlist',    [50, 100, 150, 200], ...
            'sensortypes', 'MEG, EEG', ...
            'read_all',    0);
        % Process: Power spectrum density (Welch)
        sFilesPsd = bst_process('CallProcess', 'process_psd', [sFileRaw, sFileClean], [], ...
            'timewindow',  [], ...
            'win_length',  4, ...
            'win_overlap', 50, ...
            'sensortypes', 'MEG, EEG', ...
            'edit', struct(...
                 'Comment',         'Power', ...
                 'TimeBands',       [], ...
                 'Freqs',           [], ...
                 'ClusterFuncTime', 'none', ...
                 'Measure',         'power', ...
                 'Output',          'all', ...
                 'SaveKernel',      0));
        % Process: Snapshot: Frequency spectrum
        bst_process('CallProcess', 'process_snapshot', sFilesPsd, [], ...
            'target',   10, ...  % Frequency spectrum
            'Comment',  sprintf('Power spctrum: Subject #%d, Run #%d', iSubj, iRun));

        % ===== BAD CHANNELS =====
        if ~isempty(BadChannels{iSubj}{iRun})
            % Process: Set bad channels
            bst_process('CallProcess', 'process_channel_setbad', sFileClean, [], ...
                'sensortypes', BadChannels{iSubj}{iRun});
        end

        % ===== EEG REFERENCE =====
        % Process: Re-reference EEG
        bst_process('CallProcess', 'process_eegref', sFileClean, [], ...
            'eegref',      'AVERAGE', ...
            'sensortypes', 'EEG');
    
        % ===== DETECT ARTIFACTS ======
        % Process: Detect heartbeats
        bst_process('CallProcess', 'process_evt_detect_ecg', sFileClean, [], ...
            'channelname', 'EEG063', ...
            'timewindow',  [], ...
            'eventname',   'cardiac');
        % Different amplitude thresholds for different subjects
        if strcmpi(SubjectNames{iSubj}, 'sub-05')
            thresholdMAX = 50;
        else
            thresholdMAX = 100;
        end
        % Process: Detect: blink_BAD    -   Detects all events where the amplitude exceeds 100uV
        bst_process('CallProcess', 'process_evt_detect_threshold', sFileClean, [], ...
            'eventname',    'blink_BAD', ...
            'channelname',  'EEG062', ...
            'timewindow',   [], ...
            'thresholdMAX', thresholdMAX, ...
            'units',        3, ...  % uV (10^-6)
            'bandpass',     [0.3, 20], ...
            'isAbsolute',   1, ...
            'isDCremove',   0);

        % ===== SSP COMPUTATION =====
        % Process: SSP ECG: cardiac
        bst_process('CallProcess', 'process_ssp_ecg', sFileClean, [], ...
            'eventname',   'cardiac', ...
            'sensortypes', 'MEG GRAD', ...
            'usessp',      1, ...
            'select',      SspSelect{iSubj}{iRun}{1}); 
        bst_process('CallProcess', 'process_ssp_ecg', sFileClean, [], ...
            'eventname',   'cardiac', ...
            'sensortypes', 'MEG MAG', ...
            'usessp',      1, ...
            'select',      SspSelect{iSubj}{iRun}{2});
        % Process: Snapshot: SSP projectors
        bst_process('CallProcess', 'process_snapshot', sFileClean, [], ...
            'target',   2, ...
            'Comment',  sprintf('Subject #%d, Run #%d', iSubj, iRun));   % SSP projectors
        
        % ===== IMPORT BAD EVENTS =====
        % Get bad segments: this is typically done manually, not from a script
        BadSegments = GetBadSegments(iSubj, iRun);
        % Process: Import from file
        bst_process('CallProcess', 'process_evt_import', sFileClean, [], ...
            'evtfile', {BadSegments, 'ARRAY-TIMES'}, ...
            'evtname', 'BAD');
        
        % ===== IMPORT TRIALS =====
        % Process: Import MEG/EEG: Events
        sFilesEpochs = bst_process('CallProcess', 'process_import_data_event', sFileClean, [], ...
            'subjectname', SubjectNames{iSubj}, ...
            'condition',   '', ...
            'eventname',   'Famous, Scrambled, Unfamiliar', ...
            'timewindow',  [], ...
            'epochtime',   [-0.5, 1.2], ...
            'createcond',  0, ...
            'ignoreshort', 1, ...
            'usectfcomp',  1, ...
            'usessp',      1, ...
            'freq',        [], ...
            'baseline',    [-0.5, -0.0009]);
        
        % ===== AVERAGE: RUN =====
        % Process: Average: By trial group (folder average)
        sFilesAvg = bst_process('CallProcess', 'process_average', sFilesEpochs, [], ...
            'avgtype',    5, ...  % By trial group (folder average)
            'avg_func',   1, ...  % Arithmetic average:  mean(x)
            'weighted',   0, ...
            'keepevents', 0);
        % Process: Snapshot: Recordings time series
        bst_process('CallProcess', 'process_snapshot', sFilesAvg, [], ...
            'target',   5, ...  % Recordings time series
            'modality', 4, ...  % EEG
            'time',     0.11, ...
            'Comment',  sprintf('Subject #%d, Run #%d', iSubj, iRun));
        % Process: Snapshot: Recordings topography
        bst_process('CallProcess', 'process_snapshot', sFilesAvg, [], ...
            'target',   6, ...  % Recordings topography (one time)
            'modality', 4, ...  % EEG
            'time',     0.11, ...
            'Comment',  sprintf('Subject #%d, Run #%d', iSubj, iRun));

        % ===== COMPUTE NOISECOV: EEG =====
        % Process: Compute covariance (noise or data)
        bst_process('CallProcess', 'process_noisecov', sFilesEpochs, [], ...
            'baseline',       [-0.5, -0.0009], ...
            'sensortypes',    'EEG', ...
            'target',         1, ...  % Noise covariance     (covariance over baseline time window)
            'dcoffset',       1, ...  % Block by block, to avoid effects of slow shifts in data
            'identity',       0, ...
            'copycond',       0, ...
            'copysubj',       0, ...
            'replacefile',    1);  % Replace
    end
    
    % Save report
    ReportFile = bst_report('Save', []);
    if ~isempty(reports_dir) && ~isempty(ReportFile)
        bst_report('Export', ReportFile, bst_fullfile(reports_dir, ['report_' ProtocolName '_' SubjectNames{iSubj} '.html']));
    end
end


%% ===== EMPTY ROOM RECORDINGS =====
disp(sprintf('\n===== IMPORT: EMPTY-ROOM =====\n'));
% Loop on all the noise sessions
NoiseFiles = {};
for ses = {'20090409', '20090506', '20090511', '20090515', '20090518', '20090601', '20091126', '20091208'}
    NoiseFiles{end+1} = fullfile(bids_dir, 'derivatives', 'meg_derivatives', EmptyRoomSubj, ['ses-' ses{1}], 'meg', ['sub-emptyroom_ses-' ses{1} '_task-noise_proc-sss_meg.fif']);
end
% Process: Create link to raw file
sFilesNoise = bst_process('CallProcess', 'process_import_data_raw', [], [], ...
    'subjectname',    EmptyRoomSubj, ...
    'datafile',       {NoiseFiles, 'FIF'}, ...
    'channelreplace', 1, ...
    'channelalign',   0);
% Process: Notch filter: 50Hz 100Hz 150Hz 200Hz
sFileNoiseClean = bst_process('CallProcess', 'process_notch', sFilesNoise, [], ...
        'freqlist',    [50, 100, 150, 200], ...
        'sensortypes', 'MEG, EEG', ...
        'read_all',    0);
% Process: Compute noise covariance
bst_process('CallProcess', 'process_noisecov', sFileNoiseClean, [], ...
    'baseline',    [], ...
    'sensortypes', 'MEG', ...
    'target',      1, ...  % Noise covariance     (covariance over baseline time window)
    'dcoffset',    1, ...  % Block by block, to avoid effects of slow shifts in data
    'identity',    0, ...
    'copycond',    1, ...
    'copysubj',    1, ...
    'copymatch',   1, ...
    'replacefile', 2);  % Merge
       

%% ===== SOURCE ESTIMATION =====
% Start a new report (one report for the source estimation of all the subjects)
bst_report('Start');
% Loop on the subjects: This loop is separated from the previous one, because we should 
% compute the BEM surfaces after importing all the runs, so that the registration is done 
% using the high resolution head surface, instead of the smooth scalp BEM layer.
for iSubj = 1:length(SubjectNames)
    disp(sprintf('\n===== SOURCES: SUBJECT #%d =====\n', iSubj));
    
    % ===== BEM SURFACES =====
    % Process: Generate BEM surfaces
    bst_process('CallProcess', 'process_generate_bem', [], [], ...
        'subjectname', SubjectNames{iSubj}, ...
        'nscalp',      1082, ...
        'nouter',      642, ...
        'ninner',      642, ...
        'thickness',   4);

    % ===== SELECT ALL AVERAGES =====
    % Process: Select data files in: */*
    sFilesAvg = bst_process('CallProcess', 'process_select_files_data', [], [], ...
        'subjectname',   SubjectNames{iSubj});
    % Process: Select file comments with tag: Avg
    sFilesAvg = bst_process('CallProcess', 'process_select_tag', sFilesAvg, [], ...
        'tag',    'Avg');  % Select only the files with the tag

    % ===== COMPUTE HEAD MODELS =====
    % Process: Compute head model (only for the first run of the subject)
    bst_process('CallProcess', 'process_headmodel', sFilesAvg(1), [], ...
        'sourcespace', 1, ...  % Cortex surface
        'meg',         3, ...  % Overlapping spheres
        'eeg',         3, ...  % OpenMEEG BEM
        'ecog',        1, ...  % 
        'seeg',        1, ...  % 
        'openmeeg',    struct(...
             'BemSelect',    [1, 1, 1], ...
             'BemCond',      [1, 0.0125, 1], ...
             'BemNames',     {{'Scalp', 'Skull', 'Brain'}}, ...
             'BemFiles',     {{}}, ...
             'isAdjoint',    0, ...
             'isAdaptative', 1, ...
             'isSplit',      0, ...
             'SplitLength',  4000));
    % Get all the runs for this subject (ie the list of the study indices)
    iStudyOther = setdiff(unique([sFilesAvg.iStudy]), sFilesAvg(1).iStudy);
    % Copy the forward model file to the other runs
    sHeadmodel = bst_get('HeadModelForStudy', sFilesAvg(1).iStudy);
    for iStudy = iStudyOther
        db_add(iStudy, sHeadmodel.FileName);
    end
    
    % ===== COMPUTE SOURCES: MEG =====
    % Process: Compute sources [2018]
    sAvgSrcMeg = bst_process('CallProcess', 'process_inverse_2018', sFilesAvg, [], ...
        'output',  1, ...  % Kernel only: shared
        'inverse', struct(...
             'Comment',        'MN: MEG ALL', ...
             'InverseMethod',  'minnorm', ...
             'InverseMeasure', 'amplitude', ...
             'SourceOrient',   {{'fixed'}}, ...
             'Loose',          0.2, ...
             'UseDepth',       1, ...
             'WeightExp',      0.5, ...
             'WeightLimit',    10, ...
             'NoiseMethod',    'reg', ...
             'NoiseReg',       0.1, ...
             'SnrMethod',      'fixed', ...
             'SnrRms',         1e-06, ...
             'SnrFixed',       3, ...
             'ComputeKernel',  1, ...
             'DataTypes',      {{'MEG GRAD', 'MEG MAG'}}));
    % Process: Snapshot: Sources (one time)   -   Loop only to get a correct comment for the report
    for i = 1:length(sAvgSrcMeg)
        bst_process('CallProcess', 'process_snapshot', sAvgSrcMeg(i), [], ...
            'target',         8, ...  % Sources (one time)
            'orient',         4, ...  % bottom
            'time',           0.11, ...
            'threshold',      20, ...
            'Comment',        ['MEG sources: ' sFilesAvg(i).FileName]);
    end
    
    % ===== COMPUTE SOURCES: EEG =====
    % Process: Compute sources [2018]
    sAvgSrcEeg = bst_process('CallProcess', 'process_inverse_2018', sFilesAvg, [], ...
        'output',  1, ...  % Kernel only: shared
        'inverse', struct(...
             'Comment',        'MN: EEG', ...
             'InverseMethod',  'minnorm', ...
             'InverseMeasure', 'amplitude', ...
             'SourceOrient',   {{'fixed'}}, ...
             'Loose',          0.2, ...
             'UseDepth',       1, ...
             'WeightExp',      0.5, ...
             'WeightLimit',    10, ...
             'NoiseMethod',    'reg', ...
             'NoiseReg',       0.1, ...
             'SnrMethod',      'fixed', ...
             'SnrRms',         1e-06, ...
             'SnrFixed',       3, ...
             'ComputeKernel',  1, ...
             'DataTypes',      {{'EEG'}}));
    % Process: Snapshot: Sources (one time)   -   Loop only to get a correct comment for the report
    for i = 1:length(sAvgSrcEeg)
        bst_process('CallProcess', 'process_snapshot', sAvgSrcEeg(i), [], ...
            'target',         8, ...  % Sources (one time)
            'orient',         4, ...  % bottom
            'time',           0.11, ...
            'threshold',      10, ...
            'Comment',        ['EEG sources: ' sFilesAvg(i).FileName]);
    end
end
% Save report
ReportFile = bst_report('Save', []);
if ~isempty(reports_dir) && ~isempty(ReportFile)
    bst_report('Export', ReportFile, bst_fullfile(reports_dir, ['report_' ProtocolName '_sources.html']));
end


%% ===== TIME-FREQUENCY =====
% Start a new report (one report for the time-frequency of all the subjects)
bst_report('Start');
% List of conditions to process separately
AllConditions = {'Famous', 'Scrambled', 'Unfamiliar'};
% Channels to display in the screen capture, by order of preference (if the first channel is bad, use the following)
SelChannel = {'EEG070','EEG060','EEG065','EEG050','EEG003'};
% Compute one separate time-frequency average for each subject/run/condition
for iSubj = 1:length(SubjectNames)
    disp(sprintf('\n===== TIME-FREQUENCY: SUBJECT #%d =====\n', iSubj));
    for iRun = 1:6
        % Process: Select data files in: Subject/Run
        sTrialsAll = bst_process('CallProcess', 'process_select_files_data', [], [], ...
            'subjectname',   SubjectNames{iSubj}, ...
            'condition',     sprintf('sub-%02d_ses-meg_task-facerecognition_run-%02d_proc-sss_meg_notch', iSubj, iRun));
        % Loop on the conditions
        for iCond = 1:length(AllConditions)
            % Comment describing this average
            strComment = [SubjectNames{iSubj}, ' / ', sprintf('run_%02d', iRun), ' / ', AllConditions{iCond}];
            disp(['BST> ' strComment]);
            % Find the first good channel in the display list
            if isempty(BadChannels{iSubj}{iRun})
                iSel = 1;
            else 
                iSel = find(~ismember(SelChannel,BadChannels{iSubj}{iRun}), 1);
            end
            % Process: Select file comments with tag: Avg
            sTrialsCond = bst_process('CallProcess', 'process_select_tag', sTrialsAll, [], ...
                'tag',    [AllConditions{iCond}, '_trial'], ...
                'search', 1, ...  % Search the file names
                'select', 1);  % Select only the files with the tag
            % Process: Time-frequency (Morlet wavelets), averaged across trials
            sTimefreq = bst_process('CallProcess', 'process_timefreq', sTrialsCond, [], ...
                'sensortypes', 'MEG MAG, EEG', ...
                'edit',        struct(...
                     'Comment',         ['Avg: ' AllConditions{iCond} ', Power, 6-60Hz'], ...
                     'TimeBands',       [], ...
                     'Freqs',           [6, 6.8, 7.6, 8.6, 9.7, 11, 12.4, 14, 15.8, 17.9, 20.2, 22.8, 25.7, 29, 32.7, 37, 41.7, 47.1, 53.2, 60], ...
                     'MorletFc',        1, ...
                     'MorletFwhmTc',    3, ...
                     'ClusterFuncTime', 'none', ...
                     'Measure',         'power', ...
                     'Output',          'average', ...
                     'RemoveEvoked',    0, ...
                     'SaveKernel',      0), ...
                'normalize',   'none');  % None: Save non-standardized time-frequency maps
            % Process: Extract time: [-200ms,900ms]
            sTimefreq = bst_process('CallProcess', 'process_extract_time', sTimefreq, [], ...
                'timewindow', [-0.2, 0.9], ...
                'overwrite',  1);
            % Screen capture of one sensor
            hFigTf = view_timefreq(sTimefreq.FileName, 'SingleSensor', SelChannel{iSel});
            bst_report('Snapshot', hFigTf, strComment, 'Time-frequency', [200, 200, 400, 250]);
            close(hFigTf);
        end
    end
end
% Save report
ReportFile = bst_report('Save', []);
if ~isempty(reports_dir) && ~isempty(ReportFile)
    bst_report('Export', ReportFile, bst_fullfile(reports_dir, ['report_' ProtocolName '_timefreq.html']));
end
end




%% ===== SUPPORT FUNCTIONS =====
function BadSeg = GetBadSegments(iSubj, iRun)
     BadSegments{1} = {...
         [247.867 248.185; 598.999 598.999; 598.999 598.999; 611.999 611.999; 612.999 612.999; 613.999 613.999; 616.999 616.999; 617.999 617.999; 623.999 623.999; 715.209 715.467], ...
         [84.791 85.166], ...
         [79.183 80.167], ...
         [64.309 65.185], ...
         [90.958 91.167; 178.005 178.355; 293.282 295.919; 312.298 316.479; 353.835 357.716], ...
         [60.292 66.802; 69.975 71.210; 105.233 107.586; 108.822 109.506; 376.225 376.325]};
     BadSegments{2} = {...
         [223.806 224.199; 279.772 279.895; 453.241 455.108; 692.423 692.593], ...
         [65.298 66.194; 304.727 306.178; 399.165 400.732], ...
         [203.141 205.085; 281.579 287.883; 420.395 421.128], ...
         [387.118 388.229; 440.318 441.900; 554.825 558.744], ...
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         [71.132 72.227], ...
         [98.134 98.827; 110.497 110.814; 114.000 117.272; 279.999 279.999; 279.999 279.999; 280.999 280.999; 282.999 282.999; 283.999 283.999; 284.999 284.999; 286.999 286.999; 287.999 287.999; 288.999 288.999; 289.999 289.999; 291.966 292.044; 292.999 292.999; 346.999 346.999; 437.608 437.646; 518.988 519.104; 522.969 523.015; 534.999 534.999; 536.967 537.029; 562.725 563.426]};
     BadSegments{15} = {...
         [66.755 67.172; 257.988 258.042; 258.714 259.385; 260.958 261.044; 265.931 266.062; 267.968 268.022; 268.978 269.033; 270.992 271.031; 272.964 273.017; 273.968 274.030; 275.975 276.059; 276.970 277.046; 288.976 289.038; 289.984 290.015; 295.994 296.025; 296.982 297.013; 300.966 301.152; 364.730 364.800], ...
         [46.531 46.555; 65.156 66.148; 87.535 87.642; 183.896 183.934; 294.342 294.375; 330.004 330.528; 333.785 333.815; 345.177 345.203; 399.544 399.573; 480.964 480.980], ...
         [53.557 54.175; 148.851 149.136], ...
         [43.681 44.214; 361.255 361.587; 409.462 411.021], ...
         [90.868 91.130; 410.935 411.044], ...
         [64.786 65.141; 132.385 132.786; 177.735 178.252; 278.747 278.902; 313.959 314.028; 314.970 315.031]};
     BadSegments{16} = {...
         [38.958 44.335; 305.280 312.826; 324.778 326.067; 393.183 398.367; 403.410 422.854], ...
         [49.726 50.251; 58.675 65.465; 263.918 264.088; 321.795 322.195; 522.881 523.081], ...
         [61.245 62.325; 65.628 65.905; 315.686 317.275; 335.184 336.449; 387.870 388.117; 389.892 390.062], ...
         [56.020 57.255; 60.711 61.096; 64.353 64.924; 73.202 73.757; 76.134 76.844; 95.625 96.859; 171.436 172.625; 178.359 178.715; 212.828 213.415; 352.425 352.617; 367.755 369.097; 488.400 489.426], ...
         [71.665 72.513; 76.347 77.181; 127.134 128.862], ...
         [46.190 47.209; 53.461 55.752; 194.317 194.510; 213.101 213.240; 216.356 216.442; 225.962 226.286; 245.163 245.464; 252.041 253.422; 254.648 254.856; 292.966 294.340; 340.928 341.067; 346.298 346.452]};
    BadSeg = BadSegments{iSubj}{iRun}';
end


Running scripts on a cluster

With Matlab

Matlab, including the toolboxes you need, needs to be installed on the server and a Brainstorm version needs to be located on the server. Start Brainstorm with the command "brainstorm server".

For the database: the folder "brainstorm_db" needs to be registered at the beginning of the script. You can either upload a protocol folder from your local computer, or create an empty brainstorm_db folder and a new protocol on the distance server. At the end of this initialization phase, you need to have something like the structure below:

/home/user/brainstorm3
/home/user/brainstorm_db/ProtocolName/anat
/home/user/brainstorm_db/ProtocolName/data

Your processing script could start with some of the elements below, depending on what you need:

% Start Brainstorm
cd /home/user/brainstorm3;
if ~brainstorm('status')
    brainstorm server
end

% Path to a Brainstorm database (= a folder that contains one or more Brainstorm protocols)
BrainstormDbDir = '/home/user/brainstorm_db';

% Load a new uploaded database (sets BrainstormDbDir and load all the protocols it contains)
db_import(BrainstormDbDir);

% Alternative: Set the Brainstorm DB folder
% (defines where the new protocols are going to be created, but does not load anything)
bst_set('BrainstormDbDir', BrainstormDbDir);

% Get the protocol index of an existing protocol (already loaded previously in Brainstorm)
iProtocol = bst_get('Protocol', ProtocolName);

% Create a new protocol if needed
if isempty(iProtocol)
    UseDefaultAnat = 0;
    UseDefaultChannel = 0;
    gui_brainstorm('CreateProtocol', ProtocolName, UseDefaultAnat, UseDefaultChannel);
end

% Delete an existing protocol
gui_brainstorm('DeleteProtocol', ProtocolName);

Execution: You should check that there is a Matlab license available on the server, and that RAM and disk quotas are large enough for the data you will create while processing. The Matlab version might differ from the version installed on your local computer or toolboxes might be missing, causing some errors.

A Brainstorm script can be executed either directly (it needs to start Brainstorm itself, like in the example script above), or started using the syntax brainstorm <script.m> <parameters> (starts Brainstorm in server mode, executes the script and quit Brainstorm). See section Starting Brainstorm.

Without Matlab

Brainstorm scripts can also be executed from the compiled version of Brainstorm, therefore not requiring a Matlab license, only the installation of the free MATLAB Runtime (see installation instructions, section "without Matlab"). Add the full path to the script and the parameters to the command line:

Windows: brainstorm3.bat <script.m> <parameters>
Linux/MacOS: brainstorm3.command <MATLABROOT> <script.m> <parameters>
MATLABROOT: Matlab Runtime installation folder, eg. /usr/local/MATLAB_Runtime/v98/
To avoid being asked for "brainstorm_db", add the argument: local
Example: brainstorm3.command /usr/local/MATLAB/MATLAB_Runtime/v98 main.m local

In this configuration, Brainstorm is started using the command brainstorm server and then the script is executed. Therefore, your script should not start brainstorm again: remove the line "brainstorm server" from the example script in the section above.

Finding interface callback functions

If you are looking for the function called by a menu or a button in the interface:

In Matlab, go to the "brainstorm3" folder
Click on the button "Find file" in the ribbon "Editor" of Matlab interface (Ctrl+Shift+F)
Select the option "Include subfolders"
Search for the text of the menu or button you are looking for (eg. 'Set as default'); you can do a case-sensitive or a case-insensitive search (option "Match case")
It gives you the list of all the places where this text appears in the Brainstorm code. In the previous example, in tree_callbacks.m, you’d find a call to function SetDefaultSurf.
Double-click on the corresponding line to jump to the code
Right-click on "SetDefaultSurf" > Open "SetDefaultSurf"
The editor should jump to the code of function SetDefaultSurf(), and there you’d find your call to "db_surface_default"
Right-click on it > Open "db_surface_default" to open the function and read the header that should explain its usage (this example is not very detailed, sorry)
Sometimes it helps to look at other examples of calls to this function: Use the window "Find files" again to search for text "db_surface_default"

Additional documentation

Tutorials/Scripting (last edited 2021-03-31 15:34:02 by FrancoisTadel)