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
- Find interface callback functions
- Additional quality control
- Loop over subjects
- Loop over acquisition runs
- How to process an entire study
- Final scripts
- Running scripts on a cluster
- Send report by email
- How to compile Brainstorm
- 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).
% bst_report('Email', ReportFile, username, to, subject, isFullReport);Sends the report by email, as explained in this later section: Send report by email.
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'); % 60dBEdit 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 tagWith 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
endTo 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" viewTo 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 folderExample: 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 badExample: 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 globalExample: 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 =
1Many 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.
1 function [argout1, argout2, argout3, argout4, argout5] = bst_get( varargin )
2 % BST_GET: Get a Brainstorm structure.
3 % This function is used to abstract the way that these structures are stored.
4 %
5 % USAGE :
6 % ====== DIRECTORIES ==================================================================
7 % - bst_get('UserDir') : User home directory
8 % - bst_get('BrainstormHomeDir') : Application directory of brainstorm
9 % - bst_get('BrainstormUserDir') : User home directory for brainstorm (<home>/.brainstorm/)
10 % - bst_get('BrainstormTmpDir') : User brainstorm temporary directory (Default: <home>/.brainstorm/tmp/)
11 % - bst_get('BrainstormTmpDir', isForcedDefault) : User DEFAULT brainstorm temporary directory (<home>/.brainstorm/tmp/)
12 % - bst_get('BrainstormDocDir') : Doc folder folder of the Brainstorm distribution (may vary in compiled versions)
13 % - bst_get('BrainstormDefaultsDir') : Defaults folder of the Brainstorm distribution (may vary in compiled versions)
14 % - bst_get('UserReportsDir') : User reports directory (<home>/.brainstorm/reports/)
15 % - bst_get('UserMexDir') : User temporary directory (<home>/.brainstorm/mex/)
16 % - bst_get('UserProcessDir') : User custom processes directory (<home>/.brainstorm/process/)
17 % - bst_get('UserDefaultsDir') : User defaults directory (<home>/.brainstorm/defaults/)
18 % - bst_get('UserPluginsDir') : User plugins directory (brainstorm3/plugins/ if it exists, otherwise <home>/.brainstorm/plugins/)
19 % - bst_get('BrainstormDbFile') : User brainstorm.mat file (<home>/.brainstorm/brainstorm.mat)
20 % - bst_get('BrainstormDbDir') : User database directory (contains all the brainstorm protocols)
21 % - bst_get('DirDefaultSubject') : Directory name of the default subject
22 % - bst_get('DirDefaultStudy') : Directory name of the default study for each subject
23 % - bst_get('DirAnalysisInter') : Directory name of the inter-subject analysis study
24 % - bst_get('DirAnalysisIntra') : Directory name of the intra-subject analysis study (for each subject)
25 % - bst_get('AnatomyDefaults') : Get the contents of directory bstDir/defaults/anatomy
26 % - bst_get('MniAtlasDefaults') : Get the contents of directory bstDir/defaults/mniatlas
27 % - bst_get('EegDefaults') : Get the contents of directory bstDir/defaults/eeg
28 % - bst_get('LastUsedDirs') : Structure with all the last used directories (last used)
29 % - 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)
30 % - bst_get('FileFilters', DataType) : Get the list of import filters for a specific data type
31 % - bst_get('PluginCustomPath') : Full custom path to all plugins
32 % - bst_get('BrainSuiteDir') : Full path to a local installation of BrainSuite
33 % - bst_get('SpmTpmAtlas') : Full path to the SPM atlas TPM.nii
34 % - bst_get('PythonExe') : Path to the python executable
35 %
36 % ====== PROTOCOLS ====================================================================
37 % - bst_get('iProtocol') : Indice of current protocol
38 % - bst_get('Protocol', ProtocolName): Return the indice of the protocol ProtocolName, or [] if it doesn't exist
39 % - bst_get('ProtocolInfo') : Definition structure for current protocol
40 % - bst_get('ProtocolSubjects') : Subjects list for current protocol
41 % - bst_get('ProtocolStudies') : Studies list for current protocol
42 % - bst_get('isProtocolLoaded') : 1 if the protocol has been loaded, 0 else
43 % - bst_get('isProtocolModified') : 1 if the protocol has been modified, 0 else
44 %
45 % ====== STUDIES ======================================================================
46 % - bst_get('Study', StudyFileName) : Get one study in current protocol with its file name
47 % - bst_get('Study', iStudies) : Get one or more studies
48 % - bst_get('Study') : Get current study in current protocol
49 % - bst_get('StudyCount') : Get number of studies in the current protocol
50 % - bst_get('StudyWithSubject', SubjectFile) : Find studies associated with a given subject file (WITHOUT the system studies ('intra_subject', 'default_study'))
51 % - bst_get('StudyWithSubject', ..., 'intra_subject') : Find studies ... INCLUDING 'intra_subject' study
52 % - bst_get('StudyWithSubject', ..., 'default_study') : Find studies ... INCLUDING 'default_study' study
53 % - bst_get('StudyWithCondition', ConditionPath) : Find studies for a given condition path
54 % - bst_get('ChannelStudiesWithSubject', iSubjects) : Get all the studies where there should be a channel file for a list of subjects
55 % - bst_get('AnalysisIntraStudy', iSubject) : Get the default analysis study for target subject
56 % - bst_get('AnalysisInterStudy') : Get the default analysis study for inter-subject analysis
57 % - bst_get('DefaultStudy', iSubject) : Get the default study for target subject (by subject indice)
58 % - bst_get('DefaultStudy') : Get the global default study (common to all subjects)
59 % - bst_get('DefaultStudy', SubjectFile) : Get the default study for target subject (by filename)
60 % - bst_get('ChannelFile', ChannelFile) : Find a channel file in current protocol
61 % - bst_get('ChannelFileForStudy', StudyFile/DataFile) : Find a channel file in current protocol
62 % - bst_get('ChannelForStudy', iStudies) : Return current Channel struct for target study
63 % - bst_get('ChannelModalities', ChannelFile) : Return displayable modalities for a Channel file
64 % - bst_get('ChannelModalities', DataFile) : Return displayable modalities for a Data/Results/Timefreq... file
65 % - bst_get('ChannelDevice', ChannelFile) : Return acquisistion device for a channel file
66 % - bst_get('TimefreqDisplayModalities', TfFile) : Get displayable modalities for a TF file based on recordings
67 % - bst_get('HeadModelForStudy', iStudy) : Return current HeadModel struct for target study
68 % - bst_get('HeadModelFile', HeadModelFile) : Find a HeadModel file in current protocol
69 % - bst_get('HeadModelFile', HeadModelFile, iStudies): Find a HeadModel file in current protocol
70 % - bst_get('NoiseCovFile', NoiseCovFile) : Find a noise covariance file file in current protocol
71 % - bst_get('NoiseCovFile', NoiseCovFile, iStudies) : Find a noise covariance file in current protocol
72 % - bst_get('NoiseCovFile', DataCovFile) : Find a data covariance file file in current protocol
73 % - bst_get('NoiseCovFile', DataCovFile, iStudies) : Find a data covariance file file in current protocol
74 % - bst_get('DataFile', DataFile) : Find a DataFile in current protocol
75 % - bst_get('DataFile', DataFile, iStudies) : Find a DataFile in current protocol
76 % - bst_get('DataForDataList', iStudy, DataListName) : Find all the DataFiles grouped by a data list
77 % - bst_get('DataForStudy', iStudy) : Find all the Data files that are dependent on the channel/headmodel of a given study
78 % - bst_get('DataForStudies', iStudies)
79 % - bst_get('DataForChannelFile', ChannelFile) : Find all the DataFiles that use the given ChannelFile
80 % - bst_get('ResultsFile', ResultsFile) : Find a ResultsFile in current protocol
81 % - bst_get('ResultsFile', ResultsFile, iStudies) : Find a ResultsFile in input studies
82 % - bst_get('ResultsForDataFile', DataFile, iStudies): Find all results computed based on DataFile
83 % - bst_get('StatFile', StatFile) : Find a StatFile in current protocol
84 % - bst_get('StatFile', StatFile, iStudies) : Find a StatFile in input studies
85 % - bst_get('StatForDataFile', DataFile, iStudies)
86 % - bst_get('StatForDataFile', DataFile)
87 % - bst_get('TimefreqFile', TimefreqFile)
88 % - bst_get('TimefreqFile', TimefreqFile, iStudies)
89 % - bst_get('TimefreqForFile', FileName, iStudies) : Find all timefreq files computed based on target file
90 % - bst_get('TimefreqForKernel', KernelFile)
91 % - bst_get('DipolesFile', DipolesFile)
92 % - bst_get('DipolesFile', DipolesFile, iStudies)
93 % - bst_get('DipolesForFile', FileName, iStudies) : Find all dipoles files computed based on target file
94 % - bst_get('DipolesForKernel', KernelFile)
95 % - bst_get('MatrixFile', MatrixFile)
96 % - bst_get('MatrixFile', MatrixFile, iStudies)
97 % - bst_get('MatrixForMatrixList', iStudy, MatrixListName)
98 % - bst_get('AnyFile', AnyFile)
99 % - bst_get('AnyFile', AnyFile, iStudies)
100 % - bst_get('RelatedDataFile', FileName)
101 % - bst_get('RelatedDataFile', FileName, iStudies)
102 % - bst_get('GetFilenames')
103 %
104 % ====== SUBJECTS ======================================================================
105 % - bst_get('Subject', SubjectFileName, isRaw) : Find a subject in current protocol with its file name
106 % - bst_get('Subject', SubjectName, isRaw) : Find a subject in current protocol with its name
107 % - bst_get('Subject', iSubject) : Get a subject (normal or default if iSubject==0)
108 % - bst_get('Subject') : Get current subject in current protocol
109 % - bst_get('SubjectCount') : Get number of studies in the current protocol
110 % - bst_get('NormalizedSubjectName') : Name of the subject with a normalized anatomy
111 % - bst_get('NormalizedSubject') : Get groupd analysis subject for the current protocol
112 % - bst_get('ConditionsForSubject', SubjectFile) : Find all conditions for a given subject
113 % - bst_get('SurfaceFile', SurfaceFile) : Find a surface in current protocol
114 % - bst_get('SurfaceFileByType', iSubject, SurfaceType) : Find surfaces with given type for subject #i (default only)
115 % - bst_get('SurfaceFileByType', SubjectFile, SurfaceType) : Find surfaces with given type for subject SubjectFile (default only)
116 % - bst_get('SurfaceFileByType', SurfaceName, SurfaceType) : Find surfaces with given type for subject that also has surface SurfaceName (default only)
117 % - bst_get('SurfaceFileByType', MriName, SurfaceType) : Find surfaces with given type for subject that also has MRI MriName (default only)
118 % - bst_get('SurfaceFileByType', ..., ..., isDefaultOnly) : If 0, return all the surfaces of the given type, instead of only the default surface
119 % - bst_get('MriFile', MriFile) : Find a MRI in current protocol
120 %
121 % ====== GUI =================================================================
122 % - bst_get('BstControls') : Return main Brainstorm GUI structure
123 % - bst_get('BstFrame') : Return main Brainstorm JFrame
124 % - bst_get('isGUI') : Return 1 if the Brainstorm interface is displayed
125 % - bst_get('GuiLevel') : Return GUI level: -1=server, 0=nogui, 1=normal, 2=autopilot
126 % - bst_get('ScreenDef') : Get screens configuration
127 % - bst_get('DecorationSize') : Get dimensions of the windows decorations
128 % - bst_get('Layout') : Configuration of the main Brainstorm window
129 % - bst_get('Layout', prop) : Get one property in the layout properties
130 % - bst_get('PanelContainer') : Display list of registered panel containers
131 % - bst_get('PanelContainer', ContainerName) : Get a panel container handle
132 % - bst_get('Panel') : Display list of registered panels
133 % - bst_get('Panel', PanelName) : Find a panel with its name
134 % - bst_get('PanelControls', PanelName) : Get the controls of a panel
135 % - bst_get('Clipboard') : Nodes that were copied from the interface
136 % - bst_get('FigFont') : Standard font size displayed in the figures
137 % - bst_get('Font') : Create a Java font, scaled for the operating system
138 %
139 % ====== CONFIGURATION =================================================================
140 % - bst_get('Version') : Brainstorm version
141 % - bst_get('MatlabVersion') : Matlab version (version number * 100, eg. 801)
142 % - bst_get('MatlabReleaseName') : Matlab version (release name, eg. "R2014a")
143 % - bst_get('JavaVersion') : Java version
144 % - bst_get('isJavacomponent') : Returns 1 if javacomponent is available (Matlab < 2019b), 0 otherwise
145 % - bst_get('SystemMemory') : Amount of memory available, in Mb
146 % - bst_get('ByteOrder') : {'l','b'} - Byte order used to read and save binary files
147 % - bst_get('TSDisplayMode') : {'butterfly','column'}
148 % - bst_get('ElectrodeConfig', Modality) : Structure describing the current display values for SEEG/ECOG/EEG contacts
149 % - bst_get('AutoUpdates') : {0,1} - If 1, check automatically for updates at startup
150 % - bst_get('ForceMatCompression') : {0,1} - If 1, always save mat-files using the v7 format instead of v6
151 % - bst_get('IgnoreMemoryWarnings') : {0,1} - If 1, do not display memory warnings at the Brainstorm startup
152 % - bst_get('ExpertMode') : {0,1} - If 1, show advanced options that regular user do not see
153 % - bst_get('DisplayGFP') : {0,1} - If 1, the GFP is displayed on all the time series figures
154 % - bst_get('DownsampleTimeSeries') : {0,1,...} - If > 0, downsample dense time series for faster display
155 % - bst_get('DisableOpenGL') : {0,1,2} - If 1, do not use OpenGL renderer; if 2, use software OpenGL
156 % - bst_get('InterfaceScaling') : {100,125,150,...} - Scales the Brainstorm GUI by a fixed factor
157 % - bst_get('GraphicsSmoothing') : {0,1} - If 1, uses the graphics smoothing (Matlab >= 2014b)
158 % - bst_get('SystemCopy') : {0,1} - If 1, uses the system calls mv/cp instead of movefile/copyfile (Linux only)
159 % - bst_get('DefaultFormats') : Default formats for importing/exporting data, channels, ... (last used)
160 % - bst_get('BFSProperties') : Conductivities and thicknesses for 3-shell spherical forward model
161 % - bst_get('ImportDataOptions') : Import options for recordings
162 % - bst_get('ImportEegRawOptions') : Importation options for RAW EEG format
163 % - bst_get('BugReportOptions') : Bug reporter options
164 % - bst_get('DefaultSurfaceDisplay') : Default display options for surfaces (smooth, data threshold, sulci map)
165 % - bst_get('MagneticExtrapOptions') : Structure with the options for magnetic field extrapolation
166 % - bst_get('DefaultFreqBands')
167 % - bst_get('TimefreqOptions_morlet')
168 % - bst_get('TimefreqOptions_fft')
169 % - bst_get('TimefreqOptions_psd')
170 % - bst_get('TimefreqOptions_hilbert')
171 % - bst_get('OpenMEEGOptions')
172 % - bst_get('DuneuroOptions')
173 % - bst_get('GridOptions_headmodel')
174 % - bst_get('GridOptions_dipfit')
175 % - bst_get('UniformizeTimeSeriesScales') : {0,1} - If 1, the Y-axis of all the time series figures have the scale
176 % - bst_get('FlipYAxis') : {0,1} - If 1, the recordings are displayed with the negative values UP
177 % - bst_get('AutoScaleY') : {0,1} - If 1, the axis limits are updated when the figure is updated
178 % - bst_get('ShowXGrid') : {0,1} - If 1, show the XGrid in the time series figures
179 % - bst_get('ShowYGrid') : {0,1} - If 1, show the YGrid in the time series figures
180 % - bst_get('ShowZeroLines') : {0,1} - If 1, show the Y=0 lines in the columns view
181 % - bst_get('ShowEventsMode') : {'dot','line','none'}
182 % - bst_get('Resolution') : [resX,resY] fixed resolutions for X and Y axes
183 % - bst_get('FixedScaleY', Modality) : Struct with the scales to impose on the recordings for the selected modality
184 % - bst_get('XScale', XScale) : {'log', 'linear'}
185 % - bst_get('YScale', YScale) : {'log', 'linear'}
186 % - bst_get('UseSigProcToolbox') : Use Matlab's Signal Processing Toolbox when available
187 % - bst_get('RawViewerOptions', sFile) : Display options for RAW recordings, adapt for specific file
188 % - bst_get('RawViewerOptions') : Display options for RAW recordings
189 % - bst_get('TopoLayoutOptions') : Display options for 2DLayout display
190 % - bst_get('StatThreshOptions') : Options for online statistical thresholding
191 % - bst_get('ContactSheetOptions') : Display options for contact sheets
192 % - bst_get('ProcessOptions') : Options related with the data processing
193 % - bst_get('CustomColormaps') : Gets the list of user defined colormaps
194 % - bst_get('MriOptions') : Configuration for MRI display
195 % - bst_get('DigitizeOptions') : Digitizer options
196 % - bst_get('ReadOnly') : Read only interface
197 % - bst_get('NodelistOptions') : Structure with the options for file selection in the Process1 and Process2 panels
198 % - bst_get('ResizeFunction') : Get the appropriate resize function
199 % - bst_get('groot') : Get the root graphic object
200 % - bst_get('JFrame', hFig) : Get the underlying java frame for a Matlab figure
201 % - bst_get('LastPsdDisplayFunction') : Display option of measure for spectrum (log, power, magnitude, etc.)
202 % - bst_get('PlotlyCredentials') : Get the credentials and URL to connect to plot.ly server
203 % - bst_get('ExportBidsOptions') : Additional metadata for BIDS export
204 %
205 % SEE ALSO bst_set
206
207 % @=============================================================================
208 % This function is part of the Brainstorm software:
209 % https://neuroimage.usc.edu/brainstorm
210 %
211 % Copyright (c) University of Southern California & McGill University
212 % This software is distributed under the terms of the GNU General Public License
213 % as published by the Free Software Foundation. Further details on the GPLv3
214 % license can be found at http://www.gnu.org/copyleft/gpl.html.
215 %
216 % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
217 % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
218 % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
219 % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
220 % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
221 %
222 % For more information type "brainstorm license" at command prompt.
223 % =============================================================================@
224 %
225 % Authors: Francois Tadel, 2008-2022
226 % Martin Cousineau, 2017
227
228 %% ==== PARSE INPUTS ====
229 global GlobalData;
230 if ((nargin >= 1) && ischar(varargin{1}))
231 contextName = varargin{1};
232 else
233 return
234 end
235 % Initialize returned variable
236 argout1 = [];
237 argout2 = [];
238 argout3 = [];
239 argout4 = [];
240 argout5 = [];
241
242 % Get required context structure
243 switch contextName
244 %% ==== SUBFUNCTIONS =====
245 case 'findFileInStudies'
246 [argout1, argout2, argout3] = findFileInStudies(varargin{2:end});
247
248 %% ==== BRAINSTORM CONFIGURATION ====
249 case 'Version'
250 argout1 = GlobalData.Program.Version;
251
252 case 'MatlabVersion'
253 if ~exist('version','builtin')
254 Version = 601;
255 else
256 % Get version number
257 str_vers = version();
258 vers = sscanf(str_vers, '%d.%d%*s');
259 if isempty(vers) || any(~isnumeric(vers)) || any(isnan(vers))
260 vers = 0;
261 end
262 Version = 100 * vers(1) + vers(2);
263 % Get release name
264 ipar = [find(str_vers == '('), find(str_vers == ')')];
265 end
266 argout1 = Version;
267
268 case 'MatlabReleaseName'
269 if ~exist('version','builtin')
270 Release = 'Matlab6';
271 else
272 % Get version number
273 str_vers = version();
274 % Get release name
275 ipar = [find(str_vers == '('), find(str_vers == ')')];
276 Release = str_vers(ipar(1)+1:ipar(2)-1);
277 end
278 argout1 = Release;
279
280 case 'JavaVersion'
281 strver = char(java.lang.System.getProperty('java.version'));
282 iDot = find(strver == '.');
283 if (length(iDot) < 2)
284 argout1 = str2num(strver);
285 else
286 argout1 = str2num(strver(1:iDot(2)-1));
287 end
288
289 case 'isJavacomponent'
290 % After Matlab 2019b, javacomponent() and JavaFrame property have been deprecated
291 argout1 = (bst_get('MatlabVersion') <= 906);
292
293 case 'SystemMemory'
294 maxvar = [];
295 totalmem = [];
296 if ispc && (bst_get('MatlabVersion') >= 706)
297 try
298 % Get memory info
299 usermem = memory();
300 maxvar = round(usermem.MaxPossibleArrayBytes / 1024 / 1024);
301 totalmem = round(usermem.MemAvailableAllArrays / 1024 / 1024);
302 catch
303 % Whatever...
304 end
305 end
306 argout1 = maxvar;
307 argout2 = totalmem;
308
309 case 'BrainstormHomeDir'
310 argout1 = GlobalData.Program.BrainstormHomeDir;
311 case 'BrainstormDbDir'
312 argout1 = GlobalData.DataBase.BrainstormDbDir;
313 case 'UserDir'
314 try
315 if ispc
316 userDir = getenv('USERPROFILE');
317 else
318 userDir = char(java.lang.System.getProperty('user.home'));
319 end
320 catch
321 userDir = '';
322 end
323 if isempty(userDir)
324 userDir = bst_get('BrainstormHomeDir');
325 end
326 argout1 = userDir;
327
328 case 'BrainstormUserDir'
329 bstUserDir = bst_fullfile(bst_get('UserDir'), '.brainstorm');
330 if ~isdir(bstUserDir)
331 res = mkdir(bstUserDir);
332 if ~res
333 error(['Cannot create Brainstorm user directory: "' bstUserDir '".']);
334 end
335 end
336 argout1 = bstUserDir;
337
338 case 'BrainstormTmpDir'
339 tmpDir = '';
340 isForcedDefault = ((nargin >= 2) && varargin{2});
341 % Default folder: userdir/tmp
342 defDir = bst_fullfile(bst_get('BrainstormUserDir'), 'tmp');
343 % If temporary directory is set in the preferences
344 if ~isForcedDefault && isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'BrainstormTmpDir')
345 tmpDir = GlobalData.Preferences.BrainstormTmpDir;
346 end
347 % Else: use directory userdir/tmp
348 if isempty(tmpDir)
349 tmpDir = defDir;
350 end
351 % Create directory if it does not exist yet
352 if ~isdir(tmpDir)
353 res = mkdir(tmpDir);
354 if ~res && ~strcmp(tmpDir, defDir)
355 disp(['BST> Cannot create Brainstorm temporary directory: "' tmpDir '".']);
356 disp(['BST> Using default directory instead: "' defDir '".']);
357 % Create temporary folder
358 tmpDir = defDir;
359 if ~isdir(tmpDir)
360 res = mkdir(tmpDir);
361 else
362 res = 1;
363 end
364 end
365 % Error: cannot create any temporary folder
366 if ~res
367 error(['Cannot create Brainstorm temporary directory: "' tmpDir '".']);
368 end
369 end
370 argout1 = tmpDir;
371
372 case 'BrainstormDocDir'
373 docDir = bst_fullfile(GlobalData.Program.BrainstormHomeDir, 'doc');
374 if ~exist(docDir, 'file')
375 % Matlab compiler >= 2018b stores 'doc' under 'bst_javabuil'
376 docDir = bst_fullfile(GlobalData.Program.BrainstormHomeDir, 'bst_javabuil', 'doc');
377 if ~exist(docDir, 'file')
378 docDir = '';
379 disp('BST> Could not find "doc" folder.');
380 disp(['BST> BrainstormHomeDir = ' GlobalData.Program.BrainstormHomeDir]);
381 end
382 end
383 argout1 = docDir;
384
385 case 'BrainstormDefaultsDir'
386 defaultsDir = bst_fullfile(GlobalData.Program.BrainstormHomeDir, 'defaults');
387 if ~exist(defaultsDir, 'file')
388 % Matlab compiler >= 2018b stores 'defaults' under 'bst_javabuil'
389 defaultsDir = bst_fullfile(GlobalData.Program.BrainstormHomeDir, 'bst_javabuil', 'defaults');
390 if ~exist(defaultsDir, 'file')
391 defaultsDir = '';
392 disp('BST> Could not find "defaults" folder.');
393 disp(['BST> BrainstormHomeDir = ' GlobalData.Program.BrainstormHomeDir]);
394 end
395 end
396 argout1 = defaultsDir;
397
398 case 'UserReportsDir'
399 reportDir = bst_fullfile(bst_get('BrainstormUserDir'), 'reports');
400 if ~isdir(reportDir)
401 res = mkdir(reportDir);
402 if ~res
403 error(['Cannot create user reports directory: "' reportDir '".']);
404 end
405 end
406 argout1 = reportDir;
407
408 case 'UserMexDir'
409 mexDir = bst_fullfile(bst_get('BrainstormUserDir'), 'mex');
410 if ~isdir(mexDir)
411 res = mkdir(mexDir);
412 if ~res
413 error(['Cannot create Brainstorm mex-files directory: "' mexDir '".']);
414 end
415 end
416 argout1 = mexDir;
417
418 case 'UserProcessDir'
419 processDir = bst_fullfile(bst_get('BrainstormUserDir'), 'process');
420 if ~isdir(processDir)
421 res = mkdir(processDir);
422 if ~res
423 error(['Cannot create Brainstorm custom processes directory: "' processDir '".']);
424 end
425 end
426 argout1 = processDir;
427
428 case 'UserDefaultsDir'
429 defDir = bst_fullfile(bst_get('BrainstormUserDir'), 'defaults');
430 defDirAnat = bst_fullfile(defDir, 'anatomy');
431 defDirEeg = bst_fullfile(defDir, 'eeg');
432 if ~isdir(defDir)
433 res = mkdir(defDir);
434 if ~res
435 error(['Cannot create user templates directory: "' defDir '".']);
436 end
437 end
438 if ~isdir(defDirAnat)
439 res = mkdir(defDirAnat);
440 if ~res
441 error(['Cannot create user templates directory: "' defDirAnat '".']);
442 end
443 end
444 if ~isdir(defDirEeg)
445 res = mkdir(defDirEeg);
446 if ~res
447 error(['Cannot create user templates directory: "' defDirEeg '".']);
448 end
449 end
450 argout1 = defDir;
451
452 case 'UserPluginsDir'
453 % If brainstorm/plugins exists, use it (case of an environment exported and reused)
454 pluginsDir = bst_fullfile(GlobalData.Program.BrainstormHomeDir, 'plugins');
455 % Otherwise (standard case): <home>/.brainstorm/plugins/
456 if ~exist(pluginsDir, 'file')
457 pluginsDir = bst_fullfile(bst_get('BrainstormUserDir'), 'plugins');
458 if ~isdir(pluginsDir)
459 res = mkdir(pluginsDir);
460 if ~res
461 error(['Cannot create plugins directory: "' pluginsDir '".']);
462 end
463 end
464 end
465 argout1 = pluginsDir;
466
467 case 'BrainstormDbFile'
468 argout1 = bst_fullfile(bst_get('BrainstormUserDir'), 'brainstorm.mat');
469
470 %% ==== PROTOCOL ====
471 case 'iProtocol'
472 if isempty(GlobalData.DataBase.iProtocol)
473 argout1 = 0;
474 else
475 argout1 = GlobalData.DataBase.iProtocol;
476 end
477
478 case 'Protocol'
479 if ~isempty(GlobalData.DataBase.ProtocolInfo)
480 argout1 = find(strcmpi({GlobalData.DataBase.ProtocolInfo.Comment}, varargin{2}));
481 else
482 argout1 = [];
483 end
484
485 case {'ProtocolInfo', 'ProtocolSubjects', 'ProtocolStudies', 'isProtocolLoaded', 'isProtocolModified'}
486 argout2 = GlobalData.DataBase.iProtocol;
487 % No protocol: return empty matrix
488 if isempty(argout2) || ~isnumeric(argout2) || argout2 == 0
489 return;
490 end
491 % Check index integrity
492 if ((argout2 <= 0) || (argout2 > length(GlobalData.DataBase.ProtocolInfo))), warning('Brainstorm:InvalidIndex', 'Invalid index'), return, end
493 % Get requested protocol structure
494 argout1 = GlobalData.DataBase.(contextName)(argout2);
495
496
497 %% ==== STUDY ====
498 % Usage: [sStudy, iStudy] = bst_get('Study', StudyFileName)
499 % [sStudy, iStudy] = bst_get('Study')
500 % [sStudy, iStudy] = bst_get('Study', iStudies)
501 case 'Study'
502 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
503 return;
504 end
505 % Get list of current protocols
506 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
507 ProtocolStudies = GlobalData.DataBase.ProtocolStudies(GlobalData.DataBase.iProtocol);
508 % Get list of current protocol studies
509 if isempty(ProtocolStudies) || isempty(ProtocolInfo)
510 return;
511 end
512 % ===== PARSE INPUTS =====
513 if (nargin < 2)
514 % Call: bst_get('Study');
515 iStudies = ProtocolInfo.iStudy;
516 StudyFileName = [];
517 elseif (isnumeric(varargin{2}))
518 iStudies = varargin{2};
519 StudyFileName = [];
520 elseif (ischar(varargin{2}))
521 iStudies = [];
522 StudyFileName = strrep(varargin{2}, ProtocolInfo.STUDIES, '');
523 end
524 % Indices
525 iAnalysisStudy = -2; % CANNOT USE -1 => DISABLES SEARCH FUNCTIONS
526 iDefaultStudy = -3;
527 % Indices > 0: normal studies indiced in ProtocolStudies.Study array
528
529 % ===== GET STUDY BY INDEX =====
530 % Call: bst_get('Study', iStudies);
531 if ~isempty(iStudies)
532 argout1 = repmat(ProtocolStudies.DefaultStudy, 0);
533 % Get analysis study
534 iTargetAnalysis = find(iStudies == iAnalysisStudy);
535 if ~isempty(iTargetAnalysis)
536 argout1(iTargetAnalysis) = repmat(ProtocolStudies.AnalysisStudy, size(iTargetAnalysis));
537 argout2(iTargetAnalysis) = repmat(iAnalysisStudy, size(iTargetAnalysis));
538 end
539 % Get default study
540 iTargetDefault = find(iStudies == iDefaultStudy);
541 if ~isempty(iTargetDefault)
542 argout1(iTargetDefault) = repmat(ProtocolStudies.DefaultStudy, size(iTargetDefault));
543 argout2(iTargetDefault) = repmat(iDefaultStudy, size(iTargetDefault));
544 end
545 % Get normal studies
546 iTargetNormal = find((iStudies >= 1) & (iStudies <= length(ProtocolStudies.Study)));
547 if ~isempty(iTargetNormal)
548 argout1(iTargetNormal) = ProtocolStudies.Study(iStudies(iTargetNormal));
549 argout2(iTargetNormal) = iStudies(iTargetNormal);
550 end
551 % Error
552 if isempty(argout1)
553 GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol).iStudy = [];
554 end
555
556 % ===== GET STUDY BY FILENAME =====
557 % Call: bst_get('Study', StudyFileName);
558 elseif ~isempty(StudyFileName)
559 % NORMAL STUDY
560 iStudy = find(file_compare({ProtocolStudies.Study.FileName}, StudyFileName), 1);
561 % If a study is found : return it
562 if ~isempty(iStudy)
563 argout1 = ProtocolStudies.Study(iStudy);
564 argout2 = iStudy;
565 % DEFAULT STUDY
566 elseif ~isempty(ProtocolStudies.DefaultStudy) && file_compare({ProtocolStudies.DefaultStudy.FileName}, StudyFileName)
567 argout1 = ProtocolStudies.DefaultStudy;
568 argout2 = iDefaultStudy;
569 % ANALYSIS STUDY
570 elseif ~isempty(ProtocolStudies.AnalysisStudy) && file_compare({ProtocolStudies.AnalysisStudy.FileName}, StudyFileName)
571 argout1 = ProtocolStudies.AnalysisStudy;
572 argout2 = iAnalysisStudy;
573 end
574 else
575 return
576 end
577
578
579 %% ==== STUDY WITH SUBJECT FILE ====
580 % Usage : [sStudies, iStudies] = bst_get('StudyWithSubject', SubjectFile) : WITHOUT the system studies ('intra_subject', 'default_study')
581 % [sStudies, iStudies] = bst_get(..., 'intra_subject', 'default_study') : WITH the system studies: 'intra_subject' | 'default_study'
582 case 'StudyWithSubject'
583 % Parse inputs
584 if (nargin < 2) || ~ischar(varargin{2})
585 error('Invalid call to bst_get()');
586 end
587 if (nargin > 2)
588 IntraStudies = any(strcmpi(varargin(3:end), 'intra_subject'));
589 DefaultStudies = any(strcmpi(varargin(3:end), 'default_study'));
590 else
591 IntraStudies = 0;
592 DefaultStudies = 0;
593 end
594 SubjectFile = {varargin{2}};
595 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
596 return;
597 end
598 % Get list of current protocol description
599 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
600 ProtocolStudies = GlobalData.DataBase.ProtocolStudies(GlobalData.DataBase.iProtocol);
601 if isempty(ProtocolStudies) || isempty(ProtocolInfo)
602 return;
603 end
604
605 % Get default subject
606 sDefaultSubject = bst_get('Subject', 0);
607 % If SubjectFile is the default subject filename
608 if ~isempty(sDefaultSubject) && ~isempty(sDefaultSubject.FileName) && file_compare( SubjectFile{1}, sDefaultSubject.FileName)
609 % Get all the subjects files that use default anatomy
610 ProtocolSubjects = GlobalData.DataBase.ProtocolSubjects(GlobalData.DataBase.iProtocol);
611 iSubjectUseDefaultAnat = find([ProtocolSubjects.Subject.UseDefaultAnat]);
612 if isempty(iSubjectUseDefaultAnat)
613 return
614 end
615 SubjectFile = {ProtocolSubjects.Subject(iSubjectUseDefaultAnat).FileName};
616 % Also updates inter-subject node
617 isInterSubject = 1;
618 else
619 isInterSubject = 0;
620 end
621 % Search all the current protocol's studies
622 iStudies = [];
623 for i=1:length(SubjectFile)
624 iStudies = [iStudies, find(file_compare({ProtocolStudies.Study.BrainStormSubject}, SubjectFile{i}))];
625 end
626 % Return results
627 if ~isempty(iStudies)
628 % Remove "analysis_intra" and "default_study" studies from list
629 if ~IntraStudies
630 iStudies(strcmpi({ProtocolStudies.Study(iStudies).Name}, bst_get('DirAnalysisIntra'))) = [];
631 end
632 if ~DefaultStudies
633 iStudies(strcmpi({ProtocolStudies.Study(iStudies).Name}, bst_get('DirDefaultStudy'))) = [];
634 end
635 % Return studies
636 argout1 = ProtocolStudies.Study(iStudies);
637 argout2 = iStudies;
638 else
639 argout1 = repmat(db_template('Study'), 0);
640 argout2 = [];
641 end
642 % Add inter-subject node, if needed
643 if isInterSubject
644 [sInterStudy, iInterStudy] = bst_get('AnalysisInterStudy');
645 argout1 = [argout1, sInterStudy];
646 argout2 = [argout2, iInterStudy];
647 end
648
649
650 %% ==== STUDY WITH CONDITION PATH ====
651 % USAGE: [sStudies, iStudies] = bst_get('StudyWithCondition', ConditionPath)
652 %
653 % INPUT: ConditionPath
654 % - 'SubjectName/conditionName' : Target condition for the specified subject
655 % - 'SubjectName/@intra' : Intra-subject condition for the subject
656 % - 'SubjectName/@default_study' : Default condition for the subject (where the subject's shared files are stored)
657 % - '*/conditionName' : Target condition for all the subjects
658 % - '@inter' : Inter-subject condition
659 % - '@default_study' : Protocol's default condition (where the protocol's shared files are stored)
660
661 case 'StudyWithCondition'
662 % Parse inputs
663 if (nargin ~= 2) || ~ischar(varargin{2})
664 error('Invalid call to bst_get()');
665 end
666 ConditionPath = varargin{2};
667 % Get list of current protocol description
668 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
669 ProtocolStudies = GlobalData.DataBase.ProtocolStudies(GlobalData.DataBase.iProtocol);
670 if isempty(ProtocolStudies) || isempty(ProtocolInfo)
671 return;
672 end
673
674 % ConditionPath = @inter
675 if strcmpi(ConditionPath, '@inter')
676 iStudy = -2;
677 argout2 = iStudy;
678 argout1 = bst_get('Study', iStudy);
679 % ConditionPath = @default_study
680 elseif strcmpi(ConditionPath, '@default_study')
681 iStudy = -3;
682 argout2 = iStudy;
683 argout1 = bst_get('Study', iStudy);
684 % ConditionPath = SubjectName/ConditionName
685 else
686 % Get subject and condition names
687 condSplit = str_split(ConditionPath);
688 if (length(condSplit) ~= 2)
689 error('Invalid condition path.');
690 end
691 SubjectName = condSplit{1};
692 ConditionName = condSplit{2};
693
694 % If first element is '*', search for condition in all the studies
695 if (SubjectName(1) == '*')
696 iStudies = 1:length(ProtocolStudies.Study);
697 % Else : search for condition only in studies that are linked to the subject specified in the ConditionPath
698 else
699 % Get subject
700 sSubject = bst_get('Subject', SubjectName, 1);
701 if isempty(sSubject)
702 return;
703 end
704 iStudies = find(file_compare({ProtocolStudies.Study.BrainStormSubject}, sSubject.FileName));
705 end
706 % Nothing to search
707 if isempty(iStudies)
708 return
709 end
710
711 % Search all the current protocol's studies
712 iStudies = iStudies(cellfun(@(c)isequal(ConditionName, c), [ProtocolStudies.Study(iStudies).Condition]));
713 % Return results
714 if ~isempty(iStudies)
715 % Remove "analysis_intra" and "default_study" studies from list
716 if ~strcmpi(ConditionName, '@intra')
717 iStudies(strcmpi({ProtocolStudies.Study(iStudies).Condition}, bst_get('DirAnalysisIntra'))) = [];
718 end
719 if ~strcmpi(ConditionName, '@default_study')
720 iStudies(strcmpi({ProtocolStudies.Study(iStudies).Condition}, bst_get('DirDefaultStudy'))) = [];
721 end
722 % Sort by subject
723 if (length(iStudies) > 1)
724 SubjNameList = cell(1,length(iStudies));
725 % For each study, get subject name
726 for i = 1:length(iStudies)
727 sSubject = bst_get('Subject', ProtocolStudies.Study(iStudies(i)).BrainStormSubject);
728 SubjNameList{i} = sSubject.Name;
729 end
730 % Sort subjects names
731 [sortSubjList, iSort] = sort(SubjNameList);
732 % Apply same sorting to studies
733 iStudies = iStudies(iSort);
734 end
735 % Return studies
736 argout1 = ProtocolStudies.Study(iStudies);
737 argout2 = iStudies;
738 else
739 argout1 = repmat(db_template('Study'), 0);
740 argout2 = [];
741 end
742 end
743
744 %% ==== CHANNEL STUDIES WITH SUBJECT ====
745 % Usage: iStudies = bst_get('ChannelStudiesWithSubject', iSubjects, 'NoIntra')
746 case 'ChannelStudiesWithSubject'
747 % Parse inputs
748 if (nargin >= 2) && isnumeric(varargin{2})
749 iSubjects = varargin{2};
750 else
751 error('Invalid call to bst_get()');
752 end
753 if (nargin == 3) && strcmpi(varargin{3}, 'NoIntra')
754 NoIntra = 1;
755 else
756 NoIntra = 0;
757 end
758 % Process all subjects
759 iStudies = [];
760 for i=1:length(iSubjects)
761 iSubject = iSubjects(i);
762 sSubject = bst_get('Subject', iSubject, 1);
763 % No subject: error
764 if isempty(sSubject)
765 continue
766 % If subject uses default channel file
767 elseif (sSubject.UseDefaultChannel ~= 0)
768 % Get default study for this subject
769 [tmp___, iStudiesNew] = bst_get('DefaultStudy', iSubject);
770 iStudies = [iStudies, iStudiesNew];
771 % Else: get all the studies belonging to this subject
772 else
773 if NoIntra
774 [tmp___, iStudiesNew] = bst_get('StudyWithSubject', sSubject.FileName);
775 else
776 [tmp___, iStudiesNew] = bst_get('StudyWithSubject', sSubject.FileName, 'intra_subject');
777 end
778 iStudies = [iStudies, iStudiesNew];
779 end
780 end
781 argout1 = iStudies;
782
783
784 %% ==== STUDIES COUNT ====
785 % Usage: [nbStudies] = bst_get('StudyCount')
786 case 'StudyCount'
787 % Nothing
788 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
789 argout1 = 0;
790 return;
791 end
792 % Get list of current protocol studies
793 ProtocolStudies = GlobalData.DataBase.ProtocolStudies(GlobalData.DataBase.iProtocol);
794 argout1 = length(ProtocolStudies.Study);
795
796 %% ==== SUBJECTS COUNT ====
797 % Usage: [nbSubjects] = bst_get('SubjectCount')
798 case 'SubjectCount'
799 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
800 argout1 = 0;
801 return;
802 end
803 % Get list of current protocol studies
804 ProtocolSubjects = GlobalData.DataBase.ProtocolSubjects(GlobalData.DataBase.iProtocol);
805 argout1 = length(ProtocolSubjects.Subject);
806
807 %% ==== NORMALIZED SUBJECT ====
808 case 'NormalizedSubject'
809 % Get normalized subject name
810 normSubjName = 'Group_analysis';
811 % Try to get normalized subject
812 [sNormSubj, iNormSubj] = bst_get('Subject', normSubjName, 0);
813 % If normalized subject does not exist: create it
814 if isempty(sNormSubj)
815 % Always use default anatomy
816 UseDefaultAnat = 1;
817 % If all the subjects use a global channel file: Use global default as well
818 if ~isempty(GlobalData.DataBase.ProtocolSubjects(GlobalData.DataBase.iProtocol).Subject) && ...
819 all([GlobalData.DataBase.ProtocolSubjects(GlobalData.DataBase.iProtocol).Subject.UseDefaultChannel] == 2)
820 UseDefaultChannel = 2;
821 else
822 UseDefaultChannel = 1;
823 end
824 % Create subject
825 [sNormSubj, iNormSubj] = db_add_subject(normSubjName, [], UseDefaultAnat, UseDefaultChannel);
826 % Get full subject structure
827 [sNormSubj, iNormSubj] = bst_get('Subject', normSubjName, 0);
828 end
829 argout1 = sNormSubj;
830 argout2 = iNormSubj;
831
832
833 %% ==== ANALYSIS STUDY (INTRA) ====
834 % Usage: [sAnalStudy, iAnalStudy] = bst_get('AnalysisIntraStudy', iSubject)
835 case 'AnalysisIntraStudy'
836 % Parse inputs
837 if (nargin == 2) && isnumeric(varargin{2})
838 iSubject = varargin{2};
839 else
840 error('Invalid call to bst_get()');
841 end
842 % Get subject
843 sSubject = bst_get('Subject', iSubject, 1);
844 % Get studies related to subject
845 [sSubjStudies, iSubjStudies] = bst_get('StudyWithSubject', sSubject.FileName, 'intra_subject');
846 % Look for the 'AnalysisIntra' study
847 iFound = find(cellfun(@(c)ismember(bst_get('DirAnalysisIntra'), c), {sSubjStudies.Condition}));
848 iAnalStudy = iSubjStudies(iFound);
849 sAnalStudy = sSubjStudies(iFound);
850 % Return found structure
851 argout1 = sAnalStudy;
852 argout2 = iAnalStudy;
853
854
855 %% ==== ANALYSIS STUDY (INTER) ====
856 % Usage: [sAnalStudyInter, iAnalStudyInter] = bst_get('AnalysisInterStudy')
857 case 'AnalysisInterStudy'
858 iAnalStudyInter = -2;
859 [argout1, argout2] = bst_get('Study', iAnalStudyInter);
860
861
862 %% ==== DEFAULT STUDY ====
863 % Usage: [sDefaulStudy, iDefaultStudy] = bst_get('DefaultStudy', iSubject)
864 % [sDefaulStudy, iDefaultStudy] = bst_get('DefaultStudy') : iSubject=0
865 % [sDefaulStudy, iDefaultStudy] = bst_get('DefaultStudy', SubjectFile)
866 case 'DefaultStudy'
867 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
868 return;
869 end
870 % Parse inputs
871 if (nargin == 1)
872 iSubject = 0;
873 elseif (nargin == 2) && isnumeric(varargin{2})
874 iSubject = varargin{2};
875 elseif (nargin == 2) && ischar(varargin{2})
876 SubjectFile = varargin{2};
877 % Get subject attached to study
878 [sSubject, iSubject] = bst_get('Subject', SubjectFile, 1);
879 if isempty(sSubject) || ~sSubject.UseDefaultChannel
880 return;
881 end
882 else
883 error('Invalid call to bst_get()');
884 end
885 % === DEFAULT SUBJECT ===
886 % => Return global default study
887 if (iSubject == 0)
888 % Get protocol's studies
889 ProtocolStudies = GlobalData.DataBase.ProtocolStudies(GlobalData.DataBase.iProtocol);
890 % Return Global default study
891 argout1 = ProtocolStudies.DefaultStudy;
892 argout2 = -3;
893 % === NORMAL SUBJECT ===
894 else
895 % Get subject
896 sSubject = bst_get('Subject', iSubject, 1);
897 % === GLOBAL DEFAULT STUDY ===
898 if sSubject.UseDefaultChannel == 2
899 % Get protocol's studies
900 ProtocolStudies = GlobalData.DataBase.ProtocolStudies(GlobalData.DataBase.iProtocol);
901 % Return Global default study
902 argout1 = ProtocolStudies.DefaultStudy;
903 argout2 = -3;
904 % === SUBJECT'S DEFAULT STUDY ===
905 elseif sSubject.UseDefaultChannel == 1
906 % Get studies related to subject
907 [sSubjStudies, iSubjStudies] = bst_get('StudyWithSubject', sSubject.FileName, 'default_study');
908 % Look for the 'DefaultStudy' study
909 iFound = find(cellfun(@(c)ismember(bst_get('DirDefaultStudy'), c), {sSubjStudies.Condition}));
910 iDefaultStudy = iSubjStudies(iFound);
911 sDefaultStudy = sSubjStudies(iFound);
912 % Return found structure
913 argout1 = sDefaultStudy;
914 argout2 = iDefaultStudy;
915 end
916 end
917
918
919
920 %% ==== SUBJECT ====
921 % Usage : [sSubject, iSubject] = bst_get('Subject', iSubject, isRaw)
922 % [sSubject, iSubject] = bst_get('Subject', SubjectFileName, isRaw);
923 % [sSubject, iSubject] = bst_get('Subject', SubjectName, isRaw);
924 % [sSubject, iSubject] = bst_get('Subject');
925 % If isRaw is set: force to return the real brainstormsubject description
926 % (ignoring wether it uses protocol's default anatomy or not)
927 case 'Subject'
928 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
929 return;
930 end
931 % Get list of current protocol subjects
932 ProtocolSubjects = GlobalData.DataBase.ProtocolSubjects(GlobalData.DataBase.iProtocol);
933 sSubject = [];
934 SubjectName = [];
935 SubjectFileName = [];
936 % ISRAW parameter
937 if (nargin < 3)
938 isRaw = 0;
939 else
940 isRaw = varargin{3};
941 end
942 % Call: bst_get('subject', iSubject, isRaw);
943 if (nargin >= 2) && isnumeric(varargin{2})
944 iSubject = varargin{2};
945 if (iSubject > length(ProtocolSubjects.Subject))
946 error('Invalid subject indice.');
947 end
948 % If required subject is default subject (iSubject = 0)
949 if (iSubject == 0)
950 % Default subject available
951 if ~isempty(ProtocolSubjects.DefaultSubject)
952 sSubject = ProtocolSubjects.DefaultSubject;
953 % Default subject not available
954 else
955 return
956 end
957 % Normal subject
958 else
959 sSubject = ProtocolSubjects.Subject(iSubject);
960 end
961
962 % Call: bst_get('subject', SubjectFileName, isRaw);
963 % Call: bst_get('subject', SubjectName, isRaw);
964 elseif (nargin >= 2) && isempty(varargin{2})
965 % If study name is empty: use DefaultSubject
966 SubjectFileName = ProtocolSubjects.DefaultSubject.FileName;
967 elseif (nargin >= 2) && (ischar(varargin{2}))
968 [fName, fBase, fExt] = bst_fileparts(varargin{2});
969 % Argument is a Matlab .mat filename
970 if strcmpi(fExt, '.mat')
971 SubjectFileName = varargin{2};
972 % Else : assume argument is a directory
973 else
974 SubjectName = file_standardize(varargin{2});
975 end
976
977 % Call: bst_get('subject'); => looking for current subject
978 elseif (nargin < 2)
979 % Get current subject filename in current study
980 sStudy = bst_get('Study');
981 if isempty(sStudy)
982 return
983 end
984 SubjectFileName = sStudy.BrainStormSubject;
985 % If study's subject is not defined, get DefaultSubject
986 if isempty(SubjectFileName) && ~isempty(ProtocolSubjects.DefaultSubject)
987 SubjectFileName = ProtocolSubjects.DefaultSubject.FileName;
988 end
989 else
990 error('Invalid call to bst_get()');
991 end
992
993 % If Subject is defined by its filename/name
994 if isempty(sSubject)
995 % Look in Default Subject
996 if ~isempty(ProtocolSubjects.DefaultSubject) && (file_compare(ProtocolSubjects.DefaultSubject.FileName, SubjectFileName) ...
997 || strcmpi(ProtocolSubjects.DefaultSubject.Name, SubjectName))
998 sSubject = ProtocolSubjects.DefaultSubject;
999 iSubject = 0;
1000 % If not found : find target subject file name in normal subjects
1001 elseif ~isempty(SubjectFileName)
1002 iSubject = find(file_compare({ProtocolSubjects.Subject.FileName}, SubjectFileName), 1);
1003 sSubject = ProtocolSubjects.Subject(iSubject);
1004 elseif ~isempty(SubjectName)
1005 iSubject = find(file_compare({ProtocolSubjects.Subject.Name}, SubjectName), 1);
1006 sSubject = ProtocolSubjects.Subject(iSubject);
1007 else
1008 error('Subject name not specified.');
1009 end
1010 end
1011
1012 % Return found subject
1013 if ~isempty(iSubject) && ~isempty(sSubject)
1014 % If subject uses default subject
1015 if sSubject.UseDefaultAnat && ~isRaw && ~isempty(ProtocolSubjects.DefaultSubject) && ~isempty(ProtocolSubjects.DefaultSubject.FileName)
1016 % Return default subject (WITH REAL SUBJECT'S NAME)
1017 argout1 = ProtocolSubjects.DefaultSubject;
1018 argout1.Name = sSubject.Name;
1019 argout1.UseDefaultAnat = sSubject.UseDefaultAnat;
1020 argout1.UseDefaultChannel = sSubject.UseDefaultChannel;
1021 argout2 = iSubject;
1022 % Else, return found subject
1023 else
1024 argout1 = sSubject;
1025 argout2 = iSubject;
1026 end
1027 end
1028
1029
1030 %% ==== SURFACE FILE ====
1031 % Usage : [sSubject, iSubject, iSurface] = bst_get('SurfaceFile', SurfaceFile)
1032 case 'SurfaceFile'
1033 % No protocol in database
1034 if isempty(GlobalData) || isempty(GlobalData.DataBase) || isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1035 return;
1036 end
1037 % Get list of current protocol subjects
1038 ProtocolSubjects = GlobalData.DataBase.ProtocolSubjects(GlobalData.DataBase.iProtocol);
1039 if isempty(ProtocolSubjects)
1040 return
1041 end;
1042
1043 % Parse inputs
1044 if (nargin == 2)
1045 SurfaceFile = varargin{2};
1046 else
1047 error('Invalid call to bst_get().');
1048 end
1049
1050 % Remove SUBJECTS path from SurfaceFile
1051 SurfaceFile = file_short(SurfaceFile);
1052 % Look for surface file in DefaultSubject
1053 if ~isempty(ProtocolSubjects.DefaultSubject)
1054 % Find the first surface that matches the SurfaceFile
1055 iSurface = find(file_compare(SurfaceFile, {ProtocolSubjects.DefaultSubject.Surface.FileName}), 1);
1056 % If a surface was found in default subject : return it
1057 if ~isempty(iSurface)
1058 argout1 = ProtocolSubjects.DefaultSubject;
1059 argout2 = 0;
1060 argout3 = iSurface;
1061 return
1062 end
1063 end
1064 % Look for surface file in all the surfaces of all subjects
1065 for iSubj = 1:length(ProtocolSubjects.Subject)
1066 % Find the first surface that matches the SurfaceFile
1067 iSurface = find(file_compare(SurfaceFile, {ProtocolSubjects.Subject(iSubj).Surface.FileName}), 1);
1068 % If a surface was found in current subject : return it
1069 if ~isempty(iSurface)
1070 argout1 = ProtocolSubjects.Subject(iSubj);
1071 argout2 = iSubj;
1072 argout3 = iSurface;
1073 return
1074 end
1075 end
1076
1077
1078 %% ==== SURFACE FILE BY TYPE ====
1079 % Usage : [sSurface, iSurface] = bst_get('SurfaceFileByType', iSubject, SurfaceType)
1080 % [sSurface, iSurface] = bst_get('SurfaceFileByType', SubjectFile, SurfaceType)
1081 % [sSurface, iSurface] = bst_get('SurfaceFileByType', SurfaceFile, SurfaceType)
1082 % [sSurface, iSurface] = bst_get('SurfaceFileByType', MriFile, SurfaceType)
1083 % [sSurface, iSurface] = bst_get('SurfaceFileByType', ..., SurfaceType, isDefaultOnly)
1084 case 'SurfaceFileByType'
1085 % By default: return only the default surfaces of the category
1086 if (nargin < 4)
1087 isDefaultOnly = 1;
1088 else
1089 isDefaultOnly = varargin{4};
1090 end
1091 % Get subject
1092 if isempty(varargin{2})
1093 % Get default subject
1094 sSubject = bst_get('Subject', 0);
1095 elseif ischar(varargin{2})
1096 FileName = varargin{2};
1097 sSubject = bst_get('AnyFile', FileName);
1098 else
1099 iSubject = varargin{2};
1100 sSubject = bst_get('Subject', iSubject);
1101 end
1102 % Error handling
1103 if isempty(sSubject)
1104 disp('BST> Warning: Subject not found.');
1105 return;
1106 elseif isempty(sSubject.Surface)
1107 return;
1108 end
1109 SurfaceType = varargin{3};
1110
1111 % === RETURN ONLY DEFAULTS ===
1112 if isDefaultOnly
1113 % Look for required surface type
1114 field = ['i' SurfaceType];
1115 if ~isfield(sSubject, field) || isempty(sSubject.(field))
1116 return
1117 end
1118 argout1 = sSubject.Surface(sSubject.(field));
1119 argout2 = sSubject.(field);
1120 % === RETURN ALL THE SURFACES ===
1121 else
1122 % Build the list of tagged surfaces
1123 fileTag = ['_' lower(SurfaceType)];
1124 iTargetList = find(cellfun(@(c)~isempty(strfind(c, fileTag)), {sSubject.Surface.FileName}));
1125 % Put the default cortex on top of the list
1126 iDefaults = intersect([sSubject.iCortex, sSubject.iScalp, sSubject.iInnerSkull, sSubject.iOuterSkull, sSubject.iFibers, sSubject.iFEM], iTargetList);
1127 if ~isempty(iDefaults)
1128 iTargetList = [iDefaults, setdiff(iTargetList, iDefaults)];
1129 end
1130 % Return all cortex surfaces
1131 argout1 = sSubject.Surface(iTargetList);
1132 argout2 = iTargetList;
1133 end
1134
1135
1136 %% ==== MRI FILE ====
1137 % Usage : [sSubject, iSubject, iMri] = bst_get('MriFile', MriFile)
1138 case 'MriFile'
1139 % No protocol in database
1140 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1141 return;
1142 end
1143 % Get list of current protocol subjects
1144 ProtocolSubjects = GlobalData.DataBase.ProtocolSubjects(GlobalData.DataBase.iProtocol);
1145 if isempty(ProtocolSubjects)
1146 return
1147 end
1148
1149 % Parse inputs
1150 if (nargin == 2)
1151 MriFile = varargin{2};
1152 else
1153 error('Invalid call to bst_get().');
1154 end
1155
1156 % Remove SUBJECTS path from MriFile
1157 MriFile = file_short(MriFile);
1158 % Look for MRI file in DefaultSubject
1159 if ~isempty(ProtocolSubjects.DefaultSubject)
1160 % Find the first MRI that matches the MriFile
1161 iMri = find(file_compare(MriFile, {ProtocolSubjects.DefaultSubject.Anatomy.FileName}), 1);
1162 % If a MRI was found in default subject : return it
1163 if ~isempty(iMri)
1164 argout1 = ProtocolSubjects.DefaultSubject;
1165 argout2 = 0;
1166 argout3 = iMri;
1167 return
1168 end
1169 end
1170 % Look for MRI file in all the MRIs of all subjects
1171 for iSubj = 1:length(ProtocolSubjects.Subject)
1172 % Find the first MRI that matches the MriFile
1173 iMri = find(file_compare(MriFile, {ProtocolSubjects.Subject(iSubj).Anatomy.FileName}), 1);
1174 % If a MRI was found in current subject : return it
1175 if ~isempty(iMri)
1176 argout1 = ProtocolSubjects.Subject(iSubj);
1177 argout2 = iSubj;
1178 argout3 = iMri;
1179 return
1180 end
1181 end
1182
1183
1184 %% ==== CHANNEL FILE ====
1185 % Usage: [sStudy, iStudy, iChannel] = bst_get('ChannelFile', ChannelFile)
1186 case 'ChannelFile'
1187 % No protocol in database
1188 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1189 return;
1190 end
1191 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
1192 % Parse inputs
1193 if (nargin == 2)
1194 ChannelFile = varargin{2};
1195 ChannelFile = strrep(ChannelFile, ProtocolInfo.STUDIES, '');
1196 else
1197 error('Invalid call to bst_get().');
1198 end
1199 % Look for Channel file in all the surfaces of all subjects
1200 [argout1, argout2, argout3] = findFileInStudies('Channel', 'FileName', ChannelFile);
1201
1202
1203 %% ==== CHANNEL FILE FOR STUDY ====
1204 % Usage: [ChannelFile, sStudy, iStudy] = bst_get('ChannelFileForStudy', StudyFile/DataFile)
1205 case 'ChannelFileForStudy'
1206 % Parse inputs
1207 if (nargin == 2)
1208 StudyFile = varargin{2};
1209 else
1210 error('Invalid call to bst_get().');
1211 end
1212 % Get study in database
1213 [sStudy, iStudy] = bst_get('Study', StudyFile);
1214 % If data file instead on Study file
1215 if isempty(sStudy)
1216 [sStudy, iStudy] = bst_get('AnyFile', StudyFile);
1217 end
1218 sChannel = bst_get('ChannelForStudy', iStudy);
1219 if ~isempty(sChannel)
1220 argout1 = sChannel.FileName;
1221 argout2 = sStudy;
1222 argout3 = iStudy;
1223 else
1224 argout1 = [];
1225 end
1226
1227
1228 %% ==== CHANNEL STRUCT FOR STUDY ====
1229 % Usage: [sChannel, iChanStudy] = bst_get('ChannelForStudy', iStudies)
1230 case 'ChannelForStudy'
1231 % Parse inputs
1232 if (nargin == 2)
1233 iStudies = varargin{2};
1234 else
1235 error('Invalid call to bst_get().');
1236 end
1237 iChanStudies = [];
1238 sListChannel = [];
1239 for i = 1:length(iStudies)
1240 % Get study
1241 iStudy = iStudies(i);
1242 sStudy = bst_get('Study', iStudy);
1243 if isempty(sStudy)
1244 continue;
1245 end
1246 iChanStudy = iStudy;
1247 % === Analysis-Inter node ===
1248 iAnalysisInter = -2;
1249 iGlobalDefaultStudy = -3;
1250 if (iStudy == iAnalysisInter)
1251 % If no channel file is defined in 'Analysis-intra' node: look in
1252 if isempty(sStudy.Channel)
1253 % Get global default study
1254 sStudy = bst_get('Study', iGlobalDefaultStudy);
1255 iChanStudy = iGlobalDefaultStudy;
1256 end
1257 % === All other nodes ===
1258 else
1259 % Get subject attached to study
1260 [sSubject, iSubject] = bst_get('Subject', sStudy.BrainStormSubject, 1);
1261 if isempty(sSubject)
1262 return;
1263 end
1264 % Subject uses default channel/headmodel
1265 if (sSubject.UseDefaultChannel ~= 0)
1266 [sStudy, iChanStudy] = bst_get('DefaultStudy', iSubject);
1267 if isempty(sStudy)
1268 return
1269 end
1270 end
1271 end
1272 iChanStudies = [iChanStudies, iChanStudy];
1273 sListChannel = [sListChannel, sStudy.Channel];
1274 end
1275 % Return Channel structure
1276 argout1 = sListChannel;
1277 argout2 = iChanStudies;
1278
1279 %% ==== CHANNEL MODALITIES =====
1280 % Usage: [Modalities, DispMod, DefMod] = bst_get('ChannelModalities', ChannelFile)
1281 % [Modalities, DispMod, DefMod] = bst_get('ChannelModalities', DataFile/ResultsFile/TimefreqFile...)
1282 case 'ChannelModalities'
1283 % Get input file
1284 [sStudy, iStudy, iItem, DataType, sItem] = bst_get('AnyFile', varargin{2});
1285 % If channel file
1286 if strcmpi(DataType, 'channel')
1287 sChannel = sItem;
1288 else
1289 sChannel = bst_get('ChannelForStudy', iStudy);
1290 end
1291 % Return modalities
1292 if ~isempty(sChannel)
1293 % Get all modalities
1294 if ~isempty(sChannel.DisplayableSensorTypes)
1295 % Return the displayable sensors on top of the list
1296 argout1 = cat(2, sChannel.DisplayableSensorTypes, setdiff(sChannel.Modalities, sChannel.DisplayableSensorTypes));
1297 else
1298 argout1 = sChannel.Modalities;
1299 end
1300 % Get only sensors that have spatial representation
1301 argout2 = sChannel.DisplayableSensorTypes;
1302 % Default candidates
1303 if ~isempty(argout2)
1304 defList = argout2;
1305 else
1306 defList = argout1;
1307 end
1308 if isempty(defList)
1309 return;
1310 end
1311 % Remove EDF and BDF from the default list
1312 defList = setdiff(defList, {'EDF','BDF','KDF'});
1313 % Get default modality
1314 if ismember('SEEG', defList)
1315 argout3 = 'SEEG';
1316 elseif ismember('ECOG', defList)
1317 argout3 = 'ECOG';
1318 elseif any(ismember({'MEG','MEG GRAD','MEG MAG'}, defList))
1319 argout3 = 'MEG';
1320 elseif ismember('EEG', defList)
1321 argout3 = 'EEG';
1322 elseif ismember('NIRS', defList)
1323 argout3 = 'NIRS';
1324 else
1325 argout3 = defList{1};
1326 end
1327 % Place the default on top of the lists
1328 if ismember(argout3, argout1)
1329 argout1(strcmpi(argout1, argout3)) = [];
1330 argout1 = cat(2, argout3, argout1);
1331 end
1332 if ismember(argout3, argout2)
1333 argout2(strcmpi(argout2, argout3)) = [];
1334 argout2 = cat(2, argout3, argout2);
1335 end
1336 else
1337 argout1 = [];
1338 end
1339
1340
1341 %% ==== TIMEFREQ DISPLAY MODALITIES ====
1342 % Usage: DisplayMod = bst_get('TimefreqDisplayModalities', TimefreqFile)
1343 case 'TimefreqDisplayModalities'
1344 TimefreqFile = varargin{2};
1345 % Load sensor names from file
1346 TimefreqMat = in_bst_timefreq(TimefreqFile, 0, 'RowNames');
1347 % Get channel file
1348 ChannelFile = bst_get('ChannelFileForStudy', TimefreqFile);
1349 if isempty(ChannelFile)
1350 return;
1351 end
1352 % Load channel file
1353 ChannelMat = load(file_fullpath(ChannelFile), 'Channel');
1354 % Get channels that are present in the file
1355 [tmp__,I,J] = intersect({ChannelMat.Channel.Name}, TimefreqMat.RowNames);
1356 FileMod = unique({ChannelMat.Channel(I).Type});
1357 % Check if only one type of gradiometer is selected
1358 if isequal(FileMod, {'MEG GRAD'}) && all(cellfun(@(c)(c(end)=='2'), {ChannelMat.Channel(I).Name}))
1359 argout1 = {'MEG GRAD2'};
1360 elseif isequal(FileMod, {'MEG GRAD'}) && all(cellfun(@(c)(c(end)=='3'), {ChannelMat.Channel(I).Name}))
1361 argout1 = {'MEG GRAD3'};
1362 % Keep only the modalities that can be displayed (as topography)
1363 else
1364 argout1 = intersect(FileMod, {'MEG','MEG GRAD','MEG MAG','EEG','ECOG','SEEG','NIRS'});
1365 end
1366
1367
1368 %% ==== CHANNEL DEVICE ====
1369 % Usage: Device = bst_get('ChannelDevice', ChannelFile)
1370 case 'ChannelDevice'
1371 ChannelFile = varargin{2};
1372 if ~isempty(strfind(ChannelFile, 'vectorview306'))
1373 Device = 'Vectorview306';
1374 elseif ~isempty(strfind(ChannelFile, 'ctf_acc1'))
1375 Device = 'CTF';
1376 elseif ~isempty(strfind(ChannelFile, '4d_acc1'))
1377 Device = '4D';
1378 elseif ~isempty(strfind(ChannelFile, 'babysquid'))
1379 Device = 'BabySQUID';
1380 elseif ~isempty(strfind(ChannelFile, 'babymeg'))
1381 Device = 'BabyMEG';
1382 elseif ~isempty(strfind(ChannelFile, 'kit'))
1383 Device = 'KIT';
1384 elseif ~isempty(strfind(ChannelFile, 'ricoh'))
1385 Device = 'RICOH';
1386 elseif ~isempty(strfind(ChannelFile, 'kriss'))
1387 Device = 'KRISS';
1388 elseif ~isempty(strfind(ChannelFile, 'nirsbrs'))
1389 Device = 'NIRS-BRS';
1390 else
1391 Device = '';
1392 end
1393 argout1 = Device;
1394
1395
1396 %% ==== HEADMODEL STRUCT FOR STUDY ====
1397 % Usage: [sHeadModel] = bst_get('HeadModelForStudy', iStudy)
1398 case 'HeadModelForStudy'
1399 % Parse inputs
1400 if (nargin == 2)
1401 iStudy = varargin{2};
1402 else
1403 error('Invalid call to bst_get().');
1404 end
1405 % Get study
1406 sStudy = bst_get('Study', iStudy);
1407 % === Analysis-Inter node ===
1408 iAnalysisInter = -2;
1409 iGlobalDefaultStudy = -3;
1410 if (iStudy == iAnalysisInter)
1411 % If no channel file is defined in 'Analysis-intra' node: look in
1412 if isempty(sStudy.iHeadModel)
1413 % Get global default study
1414 sStudy = bst_get('Study', iGlobalDefaultStudy);
1415 end
1416 % === All other nodes ===
1417 else
1418 % Get subject attached to study
1419 [sSubject, iSubject] = bst_get('Subject', sStudy.BrainStormSubject, 1);
1420 if isempty(sSubject)
1421 return;
1422 end
1423 % Subject uses default channel/headmodel
1424 if (sSubject.UseDefaultChannel ~= 0)
1425 sStudy = bst_get('DefaultStudy', iSubject);
1426 if isempty(sStudy)
1427 return
1428 end
1429 end
1430 end
1431 % Return HeadModel structure
1432 if ~isempty(sStudy.iHeadModel)
1433 argout1 = sStudy.HeadModel(sStudy.iHeadModel(1));
1434 else
1435 argout1 = [];
1436 end
1437
1438
1439 %% ==== HEADMODEL FILE ====
1440 % Usage: [sStudy, iStudy, iHeadModel] = bst_get('HeadModelFile', HeadModelFile, iStudies)
1441 % [sStudy, iStudy, iHeadModel] = bst_get('HeadModelFile', HeadModelFile)
1442 case 'HeadModelFile'
1443 % No protocol in database
1444 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1445 return;
1446 end
1447 % Input #2: HeadModelFile
1448 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
1449 HeadModelFile = varargin{2};
1450 HeadModelFile = strrep(HeadModelFile, ProtocolInfo.STUDIES, '');
1451 % Input #3: iStudies
1452 if (nargin < 3)
1453 iStudies = [];
1454 else
1455 iStudies = varargin{3};
1456 end
1457 % Look for surface file in all the surfaces of all subjects
1458 [argout1, argout2, argout3] = findFileInStudies('HeadModel', 'FileName', HeadModelFile, iStudies);
1459
1460 %% ==== NOISECOV FILE ====
1461 % Usage: [sStudy, iStudy, iNoiseCov] = bst_get('NoiseCovFile', NoiseCovFile, iStudies)
1462 % [sStudy, iStudy, iNoiseCov] = bst_get('NoiseCovFile', NoiseCovFile)
1463 % Usage: [sStudy, iStudy, iNoiseCov] = bst_get('DataCovFile', NoiseCovFile, iStudies)
1464 % [sStudy, iStudy, iNoiseCov] = bst_get('DataCovFile', NoiseCovFile)
1465 case {'NoiseCovFile', 'DataCovFile'}
1466 % No protocol in database
1467 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1468 return;
1469 end
1470 % Input #2: NoiseCovFile
1471 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
1472 NoiseCovFile = varargin{2};
1473 NoiseCovFile = strrep(NoiseCovFile, ProtocolInfo.STUDIES, '');
1474 % Input #3: iStudies
1475 if (nargin < 3)
1476 iStudies = [];
1477 else
1478 iStudies = varargin{3};
1479 end
1480 % Look for surface file in all the surfaces of all subjects
1481 [argout1, argout2, argout3] = findFileInStudies('NoiseCov', 'FileName', NoiseCovFile, iStudies);
1482
1483
1484 %% ==== DATA FILE ====
1485 % Usage: [sStudy, iStudy, iData] = bst_get('DataFile', DataFile, iStudies)
1486 % [sStudy, iStudy, iData] = bst_get('DataFile', DataFile)
1487 case 'DataFile'
1488 % No protocol in database
1489 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1490 return;
1491 end
1492 % Input #2: DataFile
1493 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
1494 DataFile = varargin{2};
1495 DataFile = strrep(DataFile, ProtocolInfo.STUDIES, '');
1496 % Input #3: iStudies
1497 if (nargin < 3)
1498 iStudies = [];
1499 else
1500 iStudies = varargin{3};
1501 end
1502 % Look for file in all the studies
1503 [argout1, argout2, argout3] = findFileInStudies('Data', 'FileName', DataFile, iStudies);
1504
1505
1506 %% ==== DATA FOR DATA LIST ====
1507 % Usage: [iFoundData] = bst_get('DataForDataList', iStudy, DataListName)
1508 case 'DataForDataList'
1509 iStudy = varargin{2};
1510 DataListName = varargin{3};
1511 % Get study structure
1512 sStudy = bst_get('Study', iStudy);
1513 % Get all the data files held by this datalist
1514 listComments = cellfun(@(c)deblank(str_remove_parenth(c)), {sStudy.Data.Comment}, 'UniformOutput', 0);
1515 iFoundData = find(strcmp(listComments, DataListName));
1516 % Return found data files
1517 argout1 = iFoundData;
1518
1519 %% ==== MATRIX FOR MATRIX LIST ====
1520 % Usage: [iFoundMatrix] = bst_get('MatrixForMatrixList', iStudy, MatrixListName)
1521 case 'MatrixForMatrixList'
1522 iStudy = varargin{2};
1523 MatrixListName = varargin{3};
1524 % Get study structure
1525 sStudy = bst_get('Study', iStudy);
1526 % Get all the matrix files held by this datalist
1527 listComments = cellfun(@(c)deblank(str_remove_parenth(c)), {sStudy.Matrix.Comment}, 'UniformOutput', 0);
1528 iFoundMatrix = find(strcmp(listComments, MatrixListName));
1529 % Return found matrix files
1530 argout1 = iFoundMatrix;
1531
1532
1533 %% ==== DATA FOR STUDY (INCLUDING SHARED STUDIES) ====
1534 % Usage: [iStudies, iDatas] = bst_get('DataForStudy', iStudy)
1535 case 'DataForStudy'
1536 % Get target study
1537 iStudy = varargin{2};
1538 sStudy = bst_get('Study', iStudy);
1539 isDefaultStudy = strcmpi(sStudy.Name, bst_get('DirDefaultStudy'));
1540 isGlobalDefault = (iStudy == -3);
1541
1542 % If study is the global default study
1543 sStudies = [];
1544 iStudies = [];
1545 if isGlobalDefault
1546 % Get all the subjects of the protocol
1547 nbSubjects = bst_get('SubjectCount');
1548 for iSubject = 1:nbSubjects
1549 sSubject = bst_get('Subject', iSubject, 1);
1550 if sSubject.UseDefaultChannel
1551 [tmp_sStudies, tmp_iStudies] = bst_get('StudyWithSubject', sSubject.FileName);
1552 sStudies = [sStudies, tmp_sStudies];
1553 iStudies = [iStudies, tmp_iStudies];
1554 end
1555 end
1556 % Else, if study is a subject's default study (ie. channel file is shared by all studies of one subject)
1557 elseif isDefaultStudy
1558 % Get all the subject's studies
1559 [sStudies, iStudies] = bst_get('StudyWithSubject', sStudy.BrainStormSubject, 'intra_subject', 'default_study');
1560 else
1561 % Normal: one channel per condition
1562 sStudies = sStudy;
1563 iStudies = iStudy;
1564 end
1565 % Get all the DataFiles for all these studies
1566 for i = 1:length(sStudies)
1567 nData = length(sStudies(i).Data);
1568 argout1 = [argout1, repmat(iStudies(i), [1,nData])];
1569 argout2 = [argout2, 1:nData];
1570 end
1571
1572
1573 %% ==== DATA FOR STUDIES (INCLUDING SHARED STUDIES) ====
1574 % Usage: [iStudies, iDatas] = bst_get('DataForStudies', iStudies)
1575 case 'DataForStudies'
1576 iStudies = varargin{2};
1577 for i = 1:length(iStudies)
1578 [tmp_iStudies, tmp_iDatas] = bst_get('DataForStudy', iStudies(i));
1579 argout1 = [argout1, tmp_iStudies];
1580 argout2 = [argout2, tmp_iDatas];
1581 end
1582
1583 %% ==== DATA FILE FOR CHANNEL FILE ====
1584 % Usage: DataFiles = bst_get('DataForChannelFile', ChannelFile)
1585 case 'DataForChannelFile'
1586 ChannelFile = varargin{2};
1587 DataFiles = {};
1588 % Get study for the given channel file
1589 [sStudy, iStudy] = bst_get('ChannelFile', ChannelFile);
1590 if isempty(sStudy)
1591 return;
1592 end
1593 % Get dependent data files
1594 [iStudies, iDatas] = bst_get('DataForStudy', iStudy);
1595 % Get all the Data filenames
1596 for i = 1:length(iStudies)
1597 sStudy = bst_get('Study', iStudies(i));
1598 DataFiles = cat(2, DataFiles, {sStudy.Data(iDatas(i)).FileName});
1599 end
1600 argout1 = DataFiles;
1601
1602
1603 %% ==== RESULTS FILE ====
1604 % Usage: [sStudy, iStudy, iResult] = bst_get('ResultsFile', ResultsFile, iStudies)
1605 % [sStudy, iStudy, iResult] = bst_get('ResultsFile', ResultsFile)
1606 case 'ResultsFile'
1607 % No protocol in database
1608 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1609 return;
1610 end
1611 % Input #2: ResultsFile
1612 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
1613 ResultsFile = varargin{2};
1614 ResultsFile = strrep(ResultsFile, ProtocolInfo.STUDIES, '');
1615 % Input #3: iStudies
1616 if (nargin < 3)
1617 iStudies = [];
1618 else
1619 iStudies = varargin{3};
1620 end
1621 % Look for surface file in all the surfaces of all subjects
1622 [argout1, argout2, argout3] = findFileInStudies('Result', 'FileName', ResultsFile, iStudies);
1623
1624
1625 %% ==== RESULTS FOR DATA FILE ====
1626 % Usage: [sStudy, iStudy, iResults] = bst_get('ResultsForDataFile', DataFile) : search the whole protocol
1627 % Usage: [sStudy, iStudy, iResults] = bst_get('ResultsForDataFile', DataFile, iStudies) : search only the specified studies
1628 case 'ResultsForDataFile'
1629 % No protocol in database
1630 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1631 return;
1632 end
1633 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
1634 % Input #2: DataFile
1635 DataFile = varargin{2};
1636 DataFile = strrep(DataFile, ProtocolInfo.STUDIES, '');
1637 % Determine in which studies to search for ResultsFile
1638 if (nargin >= 3)
1639 % Studies specified in argument
1640 iStudy = varargin{3};
1641 else
1642 % Get study in which DataFile is located
1643 [sStudy, iStudy] = bst_get('DataFile', DataFile);
1644 if isempty(iStudy)
1645 return;
1646 end
1647 end
1648 % Search selected studies
1649 [argout1, argout2, argout3] = findFileInStudies('Result', 'DataFile', DataFile, iStudy);
1650
1651
1652 %% ==== STAT FILE ====
1653 % Usage: [sStudy, iStudy, iData] = bst_get('StatFile', StatFile, iStudies)
1654 % [sStudy, iStudy, iData] = bst_get('StatFile', StatFile)
1655 case 'StatFile'
1656 % No protocol in database
1657 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1658 return;
1659 end
1660 % Input #2: SataFile
1661 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
1662 StatFile = varargin{2};
1663 StatFile = strrep(StatFile, ProtocolInfo.STUDIES, '');
1664 % Input #3: iStudies
1665 if (nargin < 3)
1666 iStudies = [];
1667 else
1668 iStudies = varargin{3};
1669 end
1670 % Look for surface file in all the surfaces of all subjects
1671 [argout1, argout2, argout3] = findFileInStudies('Stat', 'FileName', StatFile, iStudies);
1672
1673
1674 %% ==== STAT FOR DATA FILE ====
1675 % Usage: [sStudy, iStudy, iResults] = bst_get('StatForDataFile', DataFile) : search the whole protocol
1676 % Usage: [sStudy, iStudy, iResults] = bst_get('StatForDataFile', DataFile, iStudies) : search only the specified studies
1677 case 'StatForDataFile'
1678 % No protocol in database
1679 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1680 return;
1681 end
1682 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
1683 % Parse inputs
1684 if (nargin >= 2)
1685 DataFile = varargin{2};
1686 DataFile = strrep(DataFile, ProtocolInfo.STUDIES, '');
1687 else
1688 error('Invalid call to bst_get().');
1689 end
1690 % Determine in which studies to search for ResultsFile
1691 if (nargin >= 3)
1692 % Studies specified in argument
1693 iStudies = varargin{3};
1694 else
1695 % Get study in which DataFile is located
1696 [sStudies, iStudies] = bst_get('DataFile', DataFile);
1697 if isempty(iStudies)
1698 return;
1699 end
1700 end
1701 % Search selected studies
1702 [argout1, argout2, argout3] = findFileInStudies('Stat', 'DataFile', DataFile, iStudies);
1703
1704 %% ==== TIMEFREQ FILE ====
1705 % Usage: [sStudy, iStudy, iTimefreq] = bst_get('TimefreqFile', TimefreqFile, iStudies)
1706 % [sStudy, iStudy, iTimefreq] = bst_get('TimefreqFile', TimefreqFile)
1707 case 'TimefreqFile'
1708 % No protocol in database
1709 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1710 return;
1711 end
1712 % Input #2: TimefreqFile
1713 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
1714 TimefreqFile = varargin{2};
1715 TimefreqFile = strrep(TimefreqFile, ProtocolInfo.STUDIES, '');
1716 % Remove optional RefRowName
1717 iPipe = find(TimefreqFile == '|', 1);
1718 if ~isempty(iPipe)
1719 TimefreqFile = TimefreqFile(1:iPipe-1);
1720 end
1721 % Input #3: iStudies
1722 if (nargin < 3)
1723 iStudies = [];
1724 else
1725 iStudies = varargin{3};
1726 end
1727 % Look for surface file in all the surfaces of all subjects
1728 [argout1, argout2, argout3] = findFileInStudies('Timefreq', 'FileName', TimefreqFile, iStudies);
1729
1730 %% ==== TIMEFREQ FOR FILE ====
1731 % Usage: [sStudy, iStudy, iTimefreq] = bst_get('TimefreqForFile', FileName, iStudies) : search only the specified studies
1732 % [sStudy, iStudy, iTimefreq] = bst_get('TimefreqForFile', FileName) : search the whole protocol
1733 case 'TimefreqForFile'
1734 % No protocol in database
1735 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1736 return;
1737 end
1738 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
1739 % Parse inputs
1740 if (nargin >= 2)
1741 FileName = varargin{2};
1742 FileName = strrep(FileName, ProtocolInfo.STUDIES, '');
1743 else
1744 error('Invalid call to bst_get().');
1745 end
1746 % Get study in which file is located
1747 if (nargin >= 3)
1748 iStudies = varargin{3};
1749 [sStudy, iStudy, iFile, DataType] = bst_get('AnyFile', FileName, iStudies);
1750 else
1751 [sStudy, iStudy, iFile, DataType] = bst_get('AnyFile', FileName);
1752 end
1753 % If file was not found
1754 if isempty(iStudy)
1755 return;
1756 end
1757 % Search direct dependent files
1758 [tmp, tmp, iTf] = findFileInStudies('Timefreq', 'DataFile', FileName, iStudy);
1759 % Data files: get all the depending results, and then all the timefreq for those results
1760 if strcmpi(DataType, 'data')
1761 [tmp, tmp, iResults] = bst_get('ResultsForDataFile', FileName, iStudy);
1762 for i = 1:length(iResults);
1763 % Search selected studies
1764 [tmp, tmp, iTfRes] = findFileInStudies('Timefreq', 'DataFile', sStudy.Result(iResults(i)).FileName, iStudy);
1765 if ~isempty(iTfRes)
1766 iTf = [iTf iTfRes];
1767 end
1768 end
1769 end
1770 % Return results
1771 if ~isempty(iTf)
1772 argout1 = sStudy;
1773 argout2 = iStudy;
1774 argout3 = iTf;
1775 end
1776
1777
1778 %% ==== DIPOLES FOR FILE ====
1779 % Usage: [sStudy, iStudy, iDipoles] = bst_get('DipolesForFile', FileName, iStudies) : search only the specified studies
1780 % [sStudy, iStudy, iDipoles] = bst_get('DipolesForFile', FileName) : search the whole protocol
1781 case 'DipolesForFile'
1782 % No protocol in database
1783 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1784 return;
1785 end
1786 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
1787 % Parse inputs
1788 if (nargin >= 2)
1789 FileName = varargin{2};
1790 FileName = strrep(FileName, ProtocolInfo.STUDIES, '');
1791 else
1792 error('Invalid call to bst_get().');
1793 end
1794 % Get study in which file is located
1795 if (nargin >= 3)
1796 iStudies = varargin{3};
1797 [sStudy, iStudy, iFile, DataType] = bst_get('AnyFile', FileName, iStudies);
1798 else
1799 [sStudy, iStudy, iFile, DataType] = bst_get('AnyFile', FileName);
1800 end
1801 % If file was not found
1802 if isempty(iStudy)
1803 return;
1804 end
1805 % Search direct dependent files
1806 [tmp, tmp, iDip] = findFileInStudies('Dipoles', 'DataFile', FileName, iStudy);
1807 % Data files: get all the depending results, and then all the timefreq for those results
1808 if strcmpi(DataType, 'data')
1809 [tmp, tmp, iResults] = bst_get('ResultsForDataFile', FileName, iStudy);
1810 for i = 1:length(iResults);
1811 % Search selected studies
1812 [tmp, tmp, iDipRes] = findFileInStudies('Dipoles', 'DataFile', sStudy.Result(iResults(i)).FileName, iStudy);
1813 if ~isempty(iDipRes)
1814 iDip = [iDip, iDipRes];
1815 end
1816 end
1817 end
1818 % Return results
1819 if ~isempty(iDip)
1820 argout1 = sStudy;
1821 argout2 = iStudy;
1822 argout3 = iDip;
1823 end
1824
1825
1826 %% ==== TIMEFREQ FOR KERNEL ====
1827 % Find all the timefreq files dependent from links due to a given kernel
1828 % Usage: [sStudy, iStudy, iTimefreq] = bst_get('TimefreqForKernel', KernelFile)
1829 case 'TimefreqForKernel'
1830 sFoundStudy = [];
1831 iFoundStudy = [];
1832 iFoundTimefreq = [];
1833 % No protocol in database
1834 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1835 return;
1836 end
1837 % Get study in which file is located
1838 KernelFile = varargin{2};
1839 [sStudy, iStudy, iFile, DataType] = bst_get('ResultsFile', KernelFile);
1840 if isempty(iStudy)
1841 return;
1842 end
1843 % Get all the data files relative with this kernel
1844 [iDepStudies, iDepDatas] = bst_get('DataForStudy', iStudy);
1845 % Keep only once each study
1846 iDepStudies = unique(iDepStudies);
1847 % Process all the dependent studies
1848 for iSt = 1:length(iDepStudies)
1849 % Get the study structure
1850 sDepStudy = bst_get('Study', iDepStudies(iSt));
1851 % Process each timefreq file separately
1852 for iTf = 1:length(sDepStudy.Timefreq)
1853 DataFile = sDepStudy.Timefreq(iTf).DataFile;
1854 % Keep only the files that are linked to LINKS
1855 if isempty(DataFile) || (length(DataFile) < 5) || ~isequal(DataFile(1:5), 'link|')
1856 continue;
1857 end
1858 % Split link
1859 splitFile = str_split(DataFile, '|');
1860 % If the kernel is found: add it to the found list
1861 if file_compare(splitFile{2}, KernelFile)
1862 sFoundStudy = [sFoundStudy sDepStudy];
1863 iFoundStudy = [iFoundStudy, iDepStudies(iSt)];
1864 iFoundTimefreq = [iFoundTimefreq, iTf];
1865 end
1866 end
1867 end
1868 % Return findings
1869 argout1 = sFoundStudy;
1870 argout2 = iFoundStudy;
1871 argout3 = iFoundTimefreq;
1872
1873
1874 %% ==== DIPOLES FOR KERNEL ====
1875 % Find all the dipoles files dependent from links due to a given kernel
1876 % Usage: [sStudy, iStudy, iDipoles] = bst_get('TimefreqForKernel', KernelFile)
1877 case 'DipolesForKernel'
1878 sFoundStudy = [];
1879 iFoundStudy = [];
1880 iFoundDipoles = [];
1881 % No protocol in database
1882 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1883 return;
1884 end
1885 % Get study in which file is located
1886 KernelFile = varargin{2};
1887 [sStudy, iStudy, iFile, DataType] = bst_get('ResultsFile', KernelFile);
1888 if isempty(iStudy)
1889 return;
1890 end
1891 % Get all the data files relative with this kernel
1892 [iDepStudies, iDepDatas] = bst_get('DataForStudy', iStudy);
1893 % Keep only once each study
1894 iDepStudies = unique(iDepStudies);
1895 % Process all the dependent studies
1896 for iSt = 1:length(iDepStudies)
1897 % Get the study structure
1898 sDepStudy = bst_get('Study', iDepStudies(iSt));
1899 % Process each timefreq file separately
1900 for iDip = 1:length(sDepStudy.Dipoles)
1901 DataFile = sDepStudy.Dipoles(iDip).DataFile;
1902 % Keep only the files that are linked to LINKS
1903 if isempty(DataFile) || (length(DataFile) < 5) || ~isequal(DataFile(1:5), 'link|')
1904 continue;
1905 end
1906 % Split link
1907 splitFile = str_split(DataFile, '|');
1908 % If the kernel is found: add it to the found list
1909 if file_compare(splitFile{2}, KernelFile)
1910 sFoundStudy = [sFoundStudy sDepStudy];
1911 iFoundStudy = [iFoundStudy, iDepStudies(iSt)];
1912 iFoundDipoles = [iFoundDipoles, iDip];
1913 end
1914 end
1915 end
1916 % Return findings
1917 argout1 = sFoundStudy;
1918 argout2 = iFoundStudy;
1919 argout3 = iFoundDipoles;
1920
1921
1922 %% ==== DIPOLES FILE ====
1923 % Usage: [sStudy, iStudy, iDipole] = bst_get('DipolesFile', DipolesFile, iStudies)
1924 % [sStudy, iStudy, iDipole] = bst_get('DipolesFile', DipolesFile)
1925 case 'DipolesFile'
1926 % No protocol in database
1927 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1928 return;
1929 end
1930 % Input #2: DipolesFile
1931 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
1932 DipolesFile = varargin{2};
1933 DipolesFile = strrep(DipolesFile, ProtocolInfo.STUDIES, '');
1934 % Input #3: iStudies
1935 if (nargin < 3)
1936 iStudies = [];
1937 else
1938 iStudies = varargin{3};
1939 end
1940 % Look for surface file in all the surfaces of all subjects
1941 [argout1, argout2, argout3] = findFileInStudies('Dipoles', 'FileName', DipolesFile, iStudies);
1942
1943
1944 %% ==== MATRIX FILE ====
1945 % Usage: [sStudy, iStudy, iDipole] = bst_get('MatrixFile', MatrixFile, iStudies)
1946 % [sStudy, iStudy, iDipole] = bst_get('MatrixFile', MatrixFile)
1947 case 'MatrixFile'
1948 % No protocol in database
1949 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1950 return;
1951 end
1952 % Input #2: MatrixFile
1953 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
1954 MatrixFile = varargin{2};
1955 MatrixFile = strrep(MatrixFile, ProtocolInfo.STUDIES, '');
1956 % Input #3: iStudies
1957 if (nargin < 3)
1958 iStudies = [];
1959 else
1960 iStudies = varargin{3};
1961 end
1962 % Look for surface file in all the surfaces of all subjects
1963 [argout1, argout2, argout3] = findFileInStudies('Matrix', 'FileName', MatrixFile, iStudies);
1964
1965 %% ==== IMAGE FILE ====
1966 % Usage: [sStudy, iStudy, iDipole] = bst_get('ImageFile', ImageFile, iStudies)
1967 % [sStudy, iStudy, iDipole] = bst_get('ImageFile', ImageFile)
1968 case 'ImageFile'
1969 % No protocol in database
1970 if isempty(GlobalData.DataBase.iProtocol) || (GlobalData.DataBase.iProtocol == 0)
1971 return;
1972 end
1973 % Input #2: ImageFile
1974 ProtocolInfo = GlobalData.DataBase.ProtocolInfo(GlobalData.DataBase.iProtocol);
1975 ImageFile = varargin{2};
1976 ImageFile = strrep(ImageFile, ProtocolInfo.STUDIES, '');
1977 % Input #3: iStudies
1978 if (nargin < 3)
1979 iStudies = [];
1980 else
1981 iStudies = varargin{3};
1982 end
1983 % Look for surface file in all the surfaces of all subjects
1984 [argout1, argout2, argout3] = findFileInStudies('Image', 'FileName', ImageFile, iStudies);
1985
1986
1987 %% ==== ANY FILE ====
1988 % Usage: [sStudy, iStudy, iFile, DataType, sItem] = bst_get('AnyFile', FileName, iStudies)
1989 % [sStudy, iStudy, iFile, DataType, sItem] = bst_get('AnyFile', FileName)
1990 case 'AnyFile'
1991 % Input #2: FileName
1992 FileName = varargin{2};
1993 if isempty(FileName)
1994 return
1995 end
1996 % Input #3: iStudies
1997 if (nargin < 3)
1998 iStudies = [];
1999 else
2000 iStudies = varargin{3};
2001 end
2002 % Get data format
2003 fileType = file_gettype(FileName);
2004 if isempty(fileType)
2005 error('File type is not recognized.');
2006 end
2007 sItem = [];
2008 % Get information related with this file
2009 switch (fileType)
2010 % ===== FUNCTIONAL =====
2011 case 'channel'
2012 [sStudy, iStudy] = bst_get('ChannelFile', FileName);
2013 iItem = 1;
2014 if (nargout >= 5) && ~isempty(sStudy)
2015 sItem = sStudy.Channel;
2016 end
2017 case 'headmodel'
2018 [sStudy, iStudy, iItem] = bst_get('HeadModelFile', FileName);
2019 if (nargout >= 5) && ~isempty(sStudy)
2020 sItem = sStudy.HeadModel(iItem);
2021 end
2022 case 'noisecov'
2023 [sStudy, iStudy, iItem] = bst_get('NoiseCovFile', FileName);
2024 if (nargout >= 5) && ~isempty(sStudy)
2025 sItem = sStudy.NoiseCov(iItem);
2026 end
2027 case 'ndatacov'
2028 [sStudy, iStudy, iItem] = bst_get('DataCovFile', FileName);
2029 if (nargout >= 5) && ~isempty(sStudy)
2030 sItem = sStudy.NoiseCov(iItem);
2031 end
2032 case {'data', 'spike'}
2033 [sStudy, iStudy, iItem] = bst_get('DataFile', FileName, iStudies);
2034 if (nargout >= 5) && ~isempty(sStudy)
2035 sItem = sStudy.Data(iItem);
2036 end
2037 case {'results', 'link'}
2038 [sStudy, iStudy, iItem] = bst_get('ResultsFile', FileName, iStudies);
2039 if (nargout >= 5) && ~isempty(sStudy)
2040 sItem = sStudy.Result(iItem);
2041 end
2042 case {'presults', 'pdata','ptimefreq','pmatrix'}
2043 [sStudy, iStudy, iItem] = bst_get('StatFile', FileName, iStudies);
2044 if (nargout >= 5) && ~isempty(sStudy)
2045 sItem = sStudy.Stat(iItem);
2046 end
2047 case 'dipoles'
2048 [sStudy, iStudy, iItem] = bst_get('DipolesFile', FileName, iStudies);
2049 if (nargout >= 5) && ~isempty(sStudy)
2050 sItem = sStudy.Dipoles(iItem);
2051 end
2052 case 'timefreq'
2053 % Remove optional RefRowName
2054 iPipe = find(FileName == '|', 1);
2055 if ~isempty(iPipe)
2056 FileName = FileName(1:iPipe-1);
2057 end
2058 [sStudy, iStudy, iItem] = bst_get('TimefreqFile', FileName, iStudies);
2059 if (nargout >= 5) && ~isempty(sStudy)
2060 sItem = sStudy.Timefreq(iItem);
2061 end
2062 case 'matrix'
2063 [sStudy, iStudy, iItem] = bst_get('MatrixFile', FileName, iStudies);
2064 if (nargout >= 5) && ~isempty(sStudy)
2065 sItem = sStudy.Matrix(iItem);
2066 end
2067 case 'brainstormstudy'
2068 [sStudy, iStudy] = bst_get('Study', FileName);
2069 iItem = 0;
2070 if (nargout >= 5) && ~isempty(sStudy)
2071 sItem = sStudy;
2072 end
2073 case {'image', 'video', 'videolink'}
2074 [sStudy, iStudy, iItem] = bst_get('ImageFile', FileName, iStudies);
2075 if (nargout >= 5) && ~isempty(sStudy)
2076 sItem = sStudy.Image(iItem);
2077 end
2078 % ===== ANATOMY =====
2079 case {'cortex','scalp','innerskull','outerskull','tess','fibers','fem'}
2080 [sStudy, iStudy, iItem] = bst_get('SurfaceFile', FileName);
2081 if (nargout >= 5) && ~isempty(sStudy)
2082 sItem = sStudy.Surface(iItem);
2083 end
2084 case 'subjectimage'
2085 [sStudy, iStudy, iItem] = bst_get('MriFile', FileName);
2086 if (nargout >= 5) && ~isempty(sStudy)
2087 sItem = sStudy.Anatomy(iItem);
2088 end
2089 case 'brainstormsubject'
2090 [sStudy, iStudy] = bst_get('Subject', FileName);
2091 iItem = 0;
2092 if (nargout >= 5) && ~isempty(sStudy)
2093 sItem = sStudy;
2094 end
2095 otherwise
2096 error('File type is not recognized.');
2097 end
2098 argout1 = sStudy;
2099 argout2 = iStudy;
2100 argout3 = iItem;
2101 argout4 = fileType;
2102 if (nargout >= 5)
2103 argout5 = sItem;
2104 end
2105
2106
2107 %% ==== GET RELATED DATA FILE ====
2108 % Usage: DataFile = bst_get('RelatedDataFile', FileName, iStudies)
2109 % DataFile = bst_get('RelatedDataFile', FileName)
2110 case 'RelatedDataFile'
2111 % Input #2: FileName
2112 FileName = varargin{2};
2113 % Input #3: iStudies
2114 if (nargin < 3)
2115 iStudies = [];
2116 else
2117 iStudies = varargin{3};
2118 end
2119 % Get file in database
2120 [sStudy, iStudy, iFile, fileType] = bst_get('AnyFile', FileName, iStudies);
2121 % If this data file does not belong to any study
2122 if isempty(sStudy)
2123 return;
2124 end
2125 % Get associated data file
2126 switch (fileType)
2127 case 'data'
2128 RelatedDataFile = sStudy.Data(iFile).FileName;
2129 case {'pdata','presults','ptimefreq','pmatrix'}
2130 RelatedDataFile = sStudy.Stat(iFile).DataFile;
2131 case {'results', 'link'}
2132 RelatedDataFile = sStudy.Result(iFile).DataFile;
2133 case 'dipoles'
2134 RelatedDataFile = sStudy.Dipoles(iFile).DataFile;
2135 case 'timefreq'
2136 RelatedDataFile = sStudy.Timefreq(iFile).DataFile;
2137 otherwise
2138 RelatedDataFile = '';
2139 end
2140 % If related file is results: get related data file
2141 if ~isempty(RelatedDataFile)
2142 relFileType = file_gettype(RelatedDataFile);
2143 if ismember(relFileType, {'link','results'})
2144 RelatedDataFile = bst_get('RelatedDataFile', RelatedDataFile, iStudy);
2145 end
2146 end
2147 % Return file
2148 argout1 = RelatedDataFile;
2149
2150 %% ==== ALL CONDITIONS FOR ONE SUBJECT ====
2151 % Usage: [Conditions] = bst_get('ConditionsForSubject', SubjectFile)
2152 case 'ConditionsForSubject'
2153 % Parse inputs
2154 if (nargin == 2)
2155 SubjectFile = varargin{2};
2156 else
2157 error('Invalid call to bst_get().');
2158 end
2159 % Get list of studies associated with subject
2160 sStudies = bst_get('StudyWithSubject', SubjectFile);
2161 % Get Conditions for each study
2162 Conditions = {};
2163 for i = 1:length(sStudies)
2164 % Test if the condition of this study was not added previously
2165 isNewCondition = 1;
2166 for iCond = 1:length(Conditions)
2167 % If new condition is found
2168 % (and excludes DirAnalysisIntra and DirDefaultSubject from list)
2169 if isempty(sStudies(i).Condition) || ...
2170 isequal(sStudies(i).Condition, Conditions(iCond)) || ...
2171 strcmpi(sStudies(i).Condition{1}, bst_get('DirAnalysisIntra')) || ...
2172 strcmpi(sStudies(i).Condition{1}, bst_get('DirDefaultSubject'))
2173 isNewCondition = 0;
2174 break;
2175 end
2176 end
2177 % If Condition is not added yet : add it to the list
2178 if isNewCondition && ~isempty(sStudies(i).Condition)
2179 Conditions{end+1} = sStudies(i).Condition{1};
2180 end
2181 end
2182 % Return conditions list
2183 argout1 = Conditions;
2184
2185
2186 %% ==== ANATOMY DEFAULTS ====
2187 % Returns the list of all the anatomy defaults (distributed with the software + user defined)
2188 case 'AnatomyDefaults'
2189 % Parse inputs
2190 if (nargin == 2)
2191 AnatName = varargin{2};
2192 else
2193 AnatName = [];
2194 end
2195 % Get templates from the brainstorm3 folder
2196 progDir = bst_fullfile(bst_get('BrainstormDefaultsDir'), 'anatomy');
2197 progFiles = dir(progDir);
2198 % Get templates from the user folder
2199 userDir = bst_fullfile(bst_get('UserDefaultsDir'), 'anatomy');
2200 userFiles = dir(userDir);
2201 % Combine the two lists
2202 AllProgNames = cat(2, {progFiles.name}, cellfun(@(c)cat(2,c,'.zip'), {progFiles.name}, 'UniformOutput', 0));
2203 AllFiles = cat(2, cellfun(@(c)bst_fullfile(progDir,c), setdiff({progFiles.name}, {'.','..'}), 'UniformOutput', 0), ...
2204 cellfun(@(c)bst_fullfile(userDir,c), setdiff({userFiles.name}, AllProgNames), 'UniformOutput', 0));
2205 % Initialize list of defaults
2206 sTemplates = repmat(struct('FilePath',[],'Name',[]), 0);
2207 % Find all the valid defaults (.zip files or subdirectory with a brainstormsubject.mat in it)
2208 for i = 1:length(AllFiles)
2209 % Decompose file name
2210 [fPath, fBase, fExt] = bst_fileparts(AllFiles{i});
2211 % Entry is a directory W/ a name that does not start with a '.'
2212 if isempty(fBase) || strcmpi(fBase(1),'.') || (~isempty(fExt) && ~strcmpi(fExt, '.zip'))
2213 continue;
2214 end
2215 % If it's a folder: check for a brainstormsubject file
2216 if isdir(AllFiles{i})
2217 bstFiles = dir(bst_fullfile(AllFiles{i}, 'brainstormsubject*.mat'));
2218 if (length(bstFiles) == 1)
2219 sTemplates(end+1).FilePath = AllFiles{i};
2220 sTemplates(end).Name = fBase;
2221 end
2222 % If it's a zip file
2223 elseif isequal(fExt, '.zip')
2224 sTemplates(end+1).FilePath = AllFiles{i};
2225 sTemplates(end).Name = fBase;
2226 end
2227 end
2228 % Get defaults from internet
2229 if ~ismember('icbm152', lower({sTemplates.Name}))
2230 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=ICBM152_2019';
2231 sTemplates(end).Name = 'ICBM152';
2232 end
2233 if ~ismember('icbm152_2019', lower({sTemplates.Name}))
2234 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=ICBM152_2019';
2235 sTemplates(end).Name = 'ICBM152_2019';
2236 end
2237 if ~ismember('icbm152_brainsuite_2016', lower({sTemplates.Name}))
2238 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=ICBM152_BrainSuite_2016';
2239 sTemplates(end).Name = 'ICBM152_BrainSuite_2016';
2240 end
2241 if ~ismember('colin27_2016', lower({sTemplates.Name}))
2242 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Colin27_2016';
2243 sTemplates(end).Name = 'Colin27_2016';
2244 end
2245 if ~ismember('colin27_brainsuite_2016', lower({sTemplates.Name}))
2246 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Colin27_BrainSuite_2016';
2247 sTemplates(end).Name = 'Colin27_BrainSuite_2016';
2248 end
2249 if ~ismember('bci-dni_brainsuite_2020', lower({sTemplates.Name}))
2250 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=BCI-DNI_BrainSuite_2020';
2251 sTemplates(end).Name = 'BCI-DNI_BrainSuite_2020';
2252 end
2253 if ~ismember('uscbrain_brainsuite_2020', lower({sTemplates.Name}))
2254 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=USCBrain_BrainSuite_2020';
2255 sTemplates(end).Name = 'USCBrain_BrainSuite_2020';
2256 end
2257 if ~ismember('fsaverage_2020', lower({sTemplates.Name}))
2258 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=FSAverage_2020';
2259 sTemplates(end).Name = 'FsAverage_2020';
2260 end
2261 if ~ismember('kabdebon_7w', lower({sTemplates.Name}))
2262 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Kabdebon_7w';
2263 sTemplates(end).Name = 'Kabdebon_7w';
2264 end
2265 if ~ismember('oreilly_0.5m_2021', lower({sTemplates.Name}))
2266 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_0.5m_2021';
2267 sTemplates(end).Name = 'Oreilly_0.5m_2021';
2268 end
2269 if ~ismember('oreilly_1m_2021', lower({sTemplates.Name}))
2270 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_1m_2021';
2271 sTemplates(end).Name = 'Oreilly_1m_2021';
2272 end
2273 if ~ismember('oreilly_2m_2021', lower({sTemplates.Name}))
2274 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_2m_2021';
2275 sTemplates(end).Name = 'Oreilly_2m_2021';
2276 end
2277 if ~ismember(lower({sTemplates.Name}), 'oreilly_3m_2021')
2278 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_3m_2021';
2279 sTemplates(end).Name = 'Oreilly_3m_2021';
2280 end
2281 if ~ismember('oreilly_4.5m_2021', lower({sTemplates.Name}))
2282 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_4.5m_2021';
2283 sTemplates(end).Name = 'Oreilly_4.5m_2021';
2284 end
2285 if ~ismember('oreilly_6m_2021', lower({sTemplates.Name}))
2286 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_6m_2021';
2287 sTemplates(end).Name = 'Oreilly_6m_2021';
2288 end
2289 if ~ismember('oreilly_7.5m_2021', lower({sTemplates.Name}))
2290 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_7.5m_2021';
2291 sTemplates(end).Name = 'Oreilly_7.5m_2021';
2292 end
2293 if ~ismember('oreilly_9m_2021', lower({sTemplates.Name}))
2294 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_9m_2021';
2295 sTemplates(end).Name = 'Oreilly_9m_2021';
2296 end
2297 if ~ismember('oreilly_10.5m_2021', lower({sTemplates.Name}))
2298 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_10.5m_2021';
2299 sTemplates(end).Name = 'Oreilly_10.5m_2021';
2300 end
2301 if ~ismember('oreilly_12m_2021', lower({sTemplates.Name}))
2302 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_12m_2021';
2303 sTemplates(end).Name = 'Oreilly_12m_2021';
2304 end
2305 if ~ismember('oreilly_15m_2021', lower({sTemplates.Name}))
2306 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_15m_2021';
2307 sTemplates(end).Name = 'Oreilly_15m_2021';
2308 end
2309 if ~ismember('oreilly_18m_2021', lower({sTemplates.Name}))
2310 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_18m_2021';
2311 sTemplates(end).Name = 'Oreilly_18m_2021';
2312 end
2313 if ~ismember('oreilly_24m_2021', lower({sTemplates.Name}))
2314 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=Oreilly_24m_2021';
2315 sTemplates(end).Name = 'Oreilly_24m_2021';
2316 end
2317 % If a specific template was requested
2318 if ~isempty(AnatName)
2319 iAnat = find(strcmpi({sTemplates.Name}, AnatName));
2320 sTemplates = sTemplates(iAnat);
2321 end
2322 % Sort in alphabetical order
2323 if ~isempty(sTemplates)
2324 [tmp__, I] = sort_nat({sTemplates(2:end).Name});
2325 sTemplates = sTemplates([1, I+1]);
2326 end
2327 % Return defaults list
2328 argout1 = sTemplates;
2329
2330
2331 %% ==== MNI ATLASES ====
2332 % Returns the list of all the available MNI atlases
2333 case 'MniAtlasDefaults'
2334 % Get templates from the brainstorm3 folder
2335 mniDir = bst_fullfile(bst_get('UserDefaultsDir'), 'mniatlas');
2336 mniFiles = dir(bst_fullfile(mniDir, '*.nii.gz'));
2337 mniFiles = cellfun(@(c)bst_fullfile(mniDir,c), {mniFiles.name}, 'UniformOutput', 0);
2338 % Initialize list of defaults
2339 sTemplates = repmat(struct('FilePath',[],'Name',[],'Info',[]), 0);
2340 % Find all the valid defaults (.zip files or subdirectory with a brainstormsubject.mat in it)
2341 for i = 1:length(mniFiles)
2342 % Decompose file name
2343 [fPath, fBase, fExt] = bst_fileparts(mniFiles{i});
2344 % Keep only files with .nii and .nii.gz extensions
2345 if ~isempty(fBase) && (fBase(1) ~= '.') && ~isempty(fExt) && strcmpi(fExt, '.gz')
2346 sTemplates(end+1).FilePath = mniFiles{i};
2347 sTemplates(end).Name = strrep(fBase, '.nii', '');
2348 sTemplates(end).Info = '';
2349 end
2350 end
2351 % Sort in alphabetical order
2352 if ~isempty(sTemplates)
2353 [tmp__, I] = sort_nat(lower({sTemplates.Name}));
2354 sTemplates = sTemplates(I);
2355 end
2356
2357 % Get defaults from internet
2358 if ~ismember('aal2', lower({sTemplates.Name}))
2359 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_AAL2';
2360 sTemplates(end).Name = 'AAL2';
2361 sTemplates(end).Info = 'https://www.gin.cnrs.fr/en/tools/aal/';
2362 end
2363 if ~ismember('aal3', lower({sTemplates.Name}))
2364 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_AAL3';
2365 sTemplates(end).Name = 'AAL3';
2366 sTemplates(end).Info = 'https://www.gin.cnrs.fr/en/tools/aal/';
2367 end
2368 if ~ismember('aicha', lower({sTemplates.Name}))
2369 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_AICHA';
2370 sTemplates(end).Name = 'AICHA';
2371 sTemplates(end).Info = 'https://www.gin.cnrs.fr/en/tools/aicha';
2372 end
2373 if ~ismember('brainnetome', lower({sTemplates.Name}))
2374 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Brainnetome';
2375 sTemplates(end).Name = 'Brainnetome';
2376 sTemplates(end).Info = 'http://atlas.brainnetome.org/';
2377 end
2378 if ~ismember('brainnetome_leaddbs', lower({sTemplates.Name}))
2379 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Brainnetome_leaddbs';
2380 sTemplates(end).Name = 'Brainnetome_leaddbs';
2381 sTemplates(end).Info = 'http://atlas.brainnetome.org/';
2382 end
2383 if ~ismember('brodmann', lower({sTemplates.Name}))
2384 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Brodmann';
2385 sTemplates(end).Name = 'Brodmann';
2386 sTemplates(end).Info = 'https://people.cas.sc.edu/rorden/mricro/lesion.html#brod';
2387 end
2388 if ~ismember('hammers83', lower({sTemplates.Name}))
2389 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Hammers';
2390 sTemplates(end).Name = 'Hammers';
2391 sTemplates(end).Info = 'http://brain-development.org/brain-atlases/adult-brain-atlases/';
2392 end
2393 if ~ismember('neuromorphometrics', lower({sTemplates.Name}))
2394 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Neuromorphometrics';
2395 sTemplates(end).Name = 'Neuromorphometrics';
2396 sTemplates(end).Info = 'https://search.kg.ebrains.eu/instances/Dataset/ef48c5e9-6b3c-4d5a-a9a9-e678fe10bdf6';
2397 end
2398 if ~ismember('julich-brain-v25', lower({sTemplates.Name}))
2399 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Julich-Brain-v25';
2400 sTemplates(end).Name = 'Julich-Brain-v25';
2401 sTemplates(end).Info = 'https://search.kg.ebrains.eu/instances/Dataset/ef48c5e9-6b3c-4d5a-a9a9-e678fe10bdf6';
2402 end
2403 if ~ismember('schaefer2018_100_7net', lower({sTemplates.Name}))
2404 sTemplates(end+1).FilePath = 'http://neuroimage.usc.edu/bst/getupdate.php?t=mni_Schaefer2018';
2405 sTemplates(end).Name = 'Schaefer2018';
2406 sTemplates(end).Info = 'https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal';
2407 end
2408 % Return defaults list
2409 argout1 = sTemplates;
2410
2411
2412 %% ==== EEG DEFAULTS ====
2413 % Returns an array of struct(fullpath, name) of all the Brainstorm eeg nets defaults
2414 % Usage: EegDefaults = bst_get('EegDefaults')
2415 % EegDefaults = bst_get('EegDefaults', TemplateName=[], SetupName=[])
2416 case 'EegDefaults'
2417 % Parse inputs
2418 if (nargin >= 3)
2419 SetupName = varargin{3};
2420 else
2421 SetupName = [];
2422 end
2423 if (nargin >= 2)
2424 TemplateName = varargin{2};
2425 else
2426 TemplateName = [];
2427 end
2428 % Get templates from the brainstorm3 folder
2429 progDir = bst_fullfile(bst_get('BrainstormDefaultsDir'), 'eeg');
2430 progFiles = dir(bst_fullfile(progDir, '*'));
2431 % Get templates from the user folder
2432 userDir = bst_fullfile(bst_get('UserDefaultsDir'), 'eeg');
2433 userFiles = dir(bst_fullfile(userDir, '*'));
2434 % Combine the two lists
2435 dirList = cat(2, cellfun(@(c)bst_fullfile(progDir,c), {progFiles.name}, 'UniformOutput', 0), ...
2436 cellfun(@(c)bst_fullfile(userDir,c), setdiff({userFiles.name}, {progFiles.name}), 'UniformOutput', 0));
2437 % Initialize list of folders
2438 fullDefaultsList = repmat(struct('contents','', 'name',''), 0);
2439 % For each template directory
2440 for iDir = 1:length(dirList)
2441 % Decompose file name
2442 [fPath, fBase, fExt] = bst_fileparts(dirList{iDir});
2443 % Entry is a not a folder, or starts with a "."
2444 if ~isdir(dirList{iDir}) || isempty(fBase) || strcmpi(fBase(1),'.')
2445 continue;
2446 end
2447 % Skip if it is not the requested template
2448 if ~isempty(TemplateName) && ~strcmpi(fBase, TemplateName)
2449 continue;
2450 end
2451 % Get files list
2452 fileList = dir(bst_fullfile(dirList{iDir}, 'channel*.mat'));
2453 defaultsList = repmat(struct('fullpath','', 'name',''), 0);
2454 % Find all the valid defaults (channel files)
2455 for iFile = 1:length(fileList)
2456 [tmp__, baseName] = bst_fileparts(fileList(iFile).name);
2457 baseName = strrep(baseName, 'channel_', '');
2458 baseName = strrep(baseName, '_channel', '');
2459 baseName = strrep(baseName, '_', ' ');
2460 % Skip if it is not the requested template
2461 if ~isempty(SetupName) && ~strcmpi(baseName, SetupName)
2462 continue;
2463 end
2464 % Add to list of templates
2465 iNewDefault = length(defaultsList) + 1;
2466 defaultsList(iNewDefault).fullpath = bst_fullfile(dirList{iDir}, fileList(iFile).name);
2467 defaultsList(iNewDefault).name = baseName;
2468 end
2469 % Add files list to defaults list
2470 if ~isempty(defaultsList)
2471 fullDefaultsList(end + 1) = struct('contents', defaultsList, ...
2472 'name', fBase);
2473 end
2474 end
2475 % Return defaults list
2476 argout1 = fullDefaultsList;
2477
2478
2479 %% ==== GET FILENAMES ====
2480 case 'GetFilenames'
2481 iStudies = varargin{2};
2482 iItems = varargin{3};
2483 DataType = varargin{4};
2484 FileNames = cell(1, length(iStudies));
2485 argout1 = {};
2486 for i = 1:length(iStudies)
2487 % Get study definition
2488 sStudy = bst_get('Study', iStudies(i));
2489 if isempty(sStudy)
2490 continue;
2491 end
2492 % Recordings or sources
2493 switch (DataType)
2494 case 'data'
2495 if (iItems(i) > length(sStudy.Data))
2496 return;
2497 end
2498 FileNames{i} = sStudy.Data(iItems(i)).FileName;
2499 case 'results'
2500 if (iItems(i) > length(sStudy.Result))
2501 return;
2502 end
2503 FileNames{i} = sStudy.Result(iItems(i)).FileName;
2504 case 'timefreq'
2505 if (iItems(i) > length(sStudy.Timefreq))
2506 return;
2507 end
2508 FileNames{i} = sStudy.Timefreq(iItems(i)).FileName;
2509 case 'matrix'
2510 if (iItems(i) > length(sStudy.Matrix))
2511 return;
2512 end
2513 FileNames{i} = sStudy.Matrix(iItems(i)).FileName;
2514 case {'pdata','presults','ptimfreq'}
2515 if (iItems(i) > length(sStudy.Stat))
2516 return;
2517 end
2518 FileNames{i} = sStudy.Stat(iItems(i)).FileName;
2519 end
2520 end
2521 argout1 = FileNames;
2522
2523
2524 %% ==== GUI ====
2525 case 'BstFrame'
2526 if isempty(GlobalData) || isempty(GlobalData.Program.GUI) || isempty(GlobalData.Program.GUI.mainWindow)
2527 argout1 = [];
2528 else
2529 argout1 = GlobalData.Program.GUI.mainWindow.jBstFrame;
2530 end
2531 case 'BstControls'
2532 if isempty(GlobalData) || isempty(GlobalData.Program) || isempty(GlobalData.Program.GUI) || isempty(GlobalData.Program.GUI.mainWindow)
2533 argout1 = [];
2534 else
2535 argout1 = GlobalData.Program.GUI.mainWindow;
2536 end
2537 case 'isGUI'
2538 if isempty(GlobalData) || isempty(GlobalData.Program) || ~isfield(GlobalData.Program, 'GuiLevel')
2539 argout1 = [];
2540 else
2541 argout1 = (GlobalData.Program.GuiLevel >= 1);
2542 end
2543 case 'GuiLevel'
2544 if isempty(GlobalData) || isempty(GlobalData.Program) || ~isfield(GlobalData.Program, 'GuiLevel')
2545 argout1 = [];
2546 else
2547 argout1 = GlobalData.Program.GuiLevel;
2548 end
2549 case 'ScreenDef'
2550 if isempty(GlobalData) || isempty(GlobalData.Program) || ~isfield(GlobalData.Program, 'ScreenDef')
2551 argout1 = [];
2552 else
2553 argout1 = GlobalData.Program.ScreenDef;
2554 end
2555 case 'DecorationSize'
2556 if isempty(GlobalData) || isempty(GlobalData.Program) || ~isfield(GlobalData.Program, 'DecorationSize')
2557 argout1 = [];
2558 else
2559 argout1 = GlobalData.Program.DecorationSize;
2560 end
2561 case 'Layout'
2562 % Default or current layout structure
2563 if ~isfield(GlobalData, 'Preferences') || ~isfield(GlobalData.Preferences, 'Layout') || ~((nargin == 1) || isfield(GlobalData.Preferences.Layout, varargin{2})) || ~isfield(GlobalData.Preferences.Layout, 'MainWindowPos')
2564 GlobalData.Preferences.Layout = db_template('Layout');
2565 end
2566 % Structure or property call
2567 if (nargin == 2) && ischar(varargin{2}) && isfield(GlobalData.Preferences.Layout, varargin{2})
2568 argout1 = GlobalData.Preferences.Layout.(varargin{2});
2569 elseif (nargin == 1)
2570 argout1 = GlobalData.Preferences.Layout;
2571 else
2572 error('Invalid call to bst_get.');
2573 end
2574
2575 case 'ByteOrder'
2576 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ByteOrder')
2577 argout1 = GlobalData.Preferences.ByteOrder;
2578 else
2579 argout1 = 'l';
2580 end
2581
2582 case 'UniformizeTimeSeriesScales'
2583 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'UniformizeTimeSeriesScales')
2584 argout1 = GlobalData.Preferences.UniformizeTimeSeriesScales;
2585 else
2586 argout1 = 1;
2587 end
2588
2589 case 'FlipYAxis'
2590 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'FlipYAxis')
2591 argout1 = GlobalData.Preferences.FlipYAxis;
2592 else
2593 argout1 = 0;
2594 end
2595
2596 case 'AutoScaleY'
2597 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'AutoScaleY')
2598 argout1 = GlobalData.Preferences.AutoScaleY;
2599 else
2600 argout1 = 1;
2601 end
2602
2603 case 'ShowXGrid'
2604 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ShowXGrid')
2605 argout1 = GlobalData.Preferences.ShowXGrid;
2606 else
2607 argout1 = 0;
2608 end
2609
2610 case 'ShowYGrid'
2611 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ShowYGrid')
2612 argout1 = GlobalData.Preferences.ShowYGrid;
2613 else
2614 argout1 = 0;
2615 end
2616
2617 case 'ShowZeroLines'
2618 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ShowZeroLines')
2619 argout1 = GlobalData.Preferences.ShowZeroLines;
2620 else
2621 argout1 = 1;
2622 end
2623
2624 case 'Resolution'
2625 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'Resolution')
2626 argout1 = GlobalData.Preferences.Resolution;
2627 else
2628 argout1 = [0 0];
2629 end
2630
2631 case 'FixedScaleY'
2632 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'FixedScaleY') && isfield(GlobalData.Preferences.FixedScaleY, varargin{2}) && ~isempty(GlobalData.Preferences.FixedScaleY.(varargin{2}))
2633 argout1 = GlobalData.Preferences.FixedScaleY.(varargin{2});
2634 else
2635 argout1 = [];
2636 end
2637
2638 case 'XScale'
2639 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'XScale')
2640 argout1 = GlobalData.Preferences.XScale;
2641 else
2642 argout1 = 'linear';
2643 end
2644
2645 case 'YScale'
2646 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'YScale')
2647 argout1 = GlobalData.Preferences.YScale;
2648 else
2649 argout1 = 'linear';
2650 end
2651
2652 case 'ShowEventsMode'
2653 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ShowEventsMode')
2654 argout1 = GlobalData.Preferences.ShowEventsMode;
2655 else
2656 argout1 = 'dot';
2657 end
2658
2659 case 'AutoUpdates'
2660 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'AutoUpdates')
2661 argout1 = GlobalData.Preferences.AutoUpdates;
2662 else
2663 argout1 = 1;
2664 end
2665
2666 case 'ForceMatCompression'
2667 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ForceMatCompression')
2668 argout1 = GlobalData.Preferences.ForceMatCompression;
2669 else
2670 argout1 = 0;
2671 end
2672
2673 case 'IgnoreMemoryWarnings'
2674 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'IgnoreMemoryWarnings')
2675 argout1 = GlobalData.Preferences.IgnoreMemoryWarnings;
2676 else
2677 argout1 = 0;
2678 end
2679
2680 case 'SystemCopy'
2681 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'SystemCopy')
2682 argout1 = GlobalData.Preferences.SystemCopy;
2683 else
2684 argout1 = 0;
2685 end
2686
2687 case 'ExpertMode'
2688 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ExpertMode')
2689 argout1 = GlobalData.Preferences.ExpertMode;
2690 else
2691 argout1 = 0;
2692 end
2693
2694 case 'DisplayGFP'
2695 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'DisplayGFP')
2696 argout1 = GlobalData.Preferences.DisplayGFP;
2697 else
2698 argout1 = 1;
2699 end
2700
2701 case 'DownsampleTimeSeries'
2702 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'DownsampleTimeSeries')
2703 if (GlobalData.Preferences.DownsampleTimeSeries == 1)
2704 GlobalData.Preferences.DownsampleTimeSeries = 5;
2705 end
2706 argout1 = GlobalData.Preferences.DownsampleTimeSeries;
2707 else
2708 argout1 = 5;
2709 end
2710
2711 case 'GraphicsSmoothing'
2712 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'GraphicsSmoothing')
2713 argout1 = GlobalData.Preferences.GraphicsSmoothing;
2714 else
2715 argout1 = 5;
2716 end
2717
2718 case 'DisableOpenGL'
2719 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'DisableOpenGL')
2720 argout1 = GlobalData.Preferences.DisableOpenGL;
2721 else
2722 argout1 = 0;
2723 end
2724
2725 case 'InterfaceScaling'
2726 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'InterfaceScaling')
2727 argout1 = GlobalData.Preferences.InterfaceScaling;
2728 else
2729 % Get screen resolution
2730 if isfield(GlobalData, 'Program') && isfield(GlobalData.Program, 'ScreenDef') && isfield(GlobalData.Program.ScreenDef, 'javaPos') && ~isempty(GlobalData.Program.ScreenDef(1).javaPos)
2731 AvailableRes = [100 125 150 200 250 300 400];
2732 iRes = bst_closest(GlobalData.Program.ScreenDef(1).javaPos.width * 100 / 1920, AvailableRes);
2733 argout1 = AvailableRes(iRes);
2734 else
2735 argout1 = 100;
2736 end
2737 end
2738
2739 case 'TSDisplayMode'
2740 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'TSDisplayMode')
2741 argout1 = GlobalData.Preferences.TSDisplayMode;
2742 else
2743 argout1 = 'butterfly';
2744 end
2745
2746 case 'PluginCustomPath'
2747 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'PluginCustomPath') && ~isempty(GlobalData.Preferences.PluginCustomPath)
2748 argout1 = GlobalData.Preferences.PluginCustomPath;
2749 else
2750 argout1 = [];
2751 end
2752
2753 case 'BrainSuiteDir'
2754 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'BrainSuiteDir') && ~isempty(GlobalData.Preferences.BrainSuiteDir)
2755 if isdir(GlobalData.Preferences.BrainSuiteDir) && file_exist(bst_fullfile(GlobalData.Preferences.BrainSuiteDir, 'bdp'))
2756 argout1 = GlobalData.Preferences.BrainSuiteDir;
2757 else
2758 argout1 = [];
2759 end
2760 else
2761 argout1 = [];
2762 end
2763
2764 case 'SpmTpmAtlas'
2765 % Get template file
2766 tpmUser = bst_fullfile(bst_get('BrainstormUserDir'), 'defaults', 'spm', 'TPM.nii');
2767 if file_exist(tpmUser)
2768 argout1 = tpmUser;
2769 disp(['SPM12 template found: ' tpmUser]);
2770 return;
2771 end
2772 % If it does not exist: check in brainstorm3 folder
2773 tpmDistrib = bst_fullfile(bst_get('BrainstormHomeDir'), 'defaults', 'spm', 'TPM.nii');
2774 if file_exist(tpmDistrib)
2775 argout1 = tpmDistrib;
2776 disp(['SPM12 template found: ' tpmDistrib]);
2777 return;
2778 end
2779 % If it does not exist: check in spm12 folder
2780 PlugSpm = bst_plugin('GetInstalled', 'spm12');
2781 if ~isempty(PlugSpm)
2782 tpmSpm = bst_fullfile(PlugSpm.Path, PlugSpm.SubFolder, 'tpm', 'TPM.nii');
2783 if file_exist(tpmSpm)
2784 argout1 = tpmSpm;
2785 disp(['SPM12 template found: ' tpmSpm]);
2786 return;
2787 end
2788 else
2789 tpmSpm = '';
2790 end
2791 % Not found...
2792 disp('SPM12 template not found in any of the following folders:');
2793 disp([' - ' tpmUser]);
2794 disp([' - ' tpmDistrib]);
2795 if ~isempty(tpmSpm)
2796 disp([' - ' tpmSpm]);
2797 end
2798 % Return the preferred location: .brainstorm/defaults/spm/TPM.nii
2799 argout1 = tpmUser;
2800
2801 case 'PythonExe'
2802 % Get saved value
2803 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'PythonExe') && ~isempty(GlobalData.Preferences.PythonExe)
2804 if file_exist(GlobalData.Preferences.PythonExe)
2805 argout1 = GlobalData.Preferences.PythonExe;
2806 else
2807 disp(['BST> Error: Python executable not found: ' GlobalData.Preferences.PythonExe]);
2808 argout1 = [];
2809 end
2810 else
2811 argout1 = [];
2812 end
2813 % If not defined in Brainstorm, but set in Matlab
2814 if isempty(argout1)
2815 [pyVer, PythonExe] = bst_python_ver();
2816 if ~isempty(PythonExe) && file_exist(PythonExe)
2817 disp(['BST> Found Python executable: ' PythonExe]);
2818 argout1 = PythonExe;
2819 bst_set('PythonExe', PythonExe);
2820 end
2821 end
2822
2823 case 'ElectrodeConfig'
2824 % Get modality
2825 Modality = varargin{2};
2826 if isempty(Modality) || ~ismember(Modality, {'EEG','ECOG','SEEG','ECOG+SEEG'})
2827 disp(['GET> Invalid modality: ' Modality]);
2828 Modality = 'EEG';
2829 end
2830 % Value was saved previously
2831 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'ElectrodeConfig') && isfield(GlobalData.Preferences.ElectrodeConfig, Modality) && isfield(GlobalData.Preferences.ElectrodeConfig.(Modality), 'ContactDiameter')
2832 argout1 = GlobalData.Preferences.ElectrodeConfig.(Modality);
2833 % Get default value
2834 else
2835 switch (Modality)
2836 case 'EEG'
2837 ElectrodeConfig.Type = 'eeg';
2838 ElectrodeConfig.ContactDiameter = 0.010;
2839 ElectrodeConfig.ContactLength = 0.002;
2840 ElectrodeConfig.ElecDiameter = [];
2841 ElectrodeConfig.ElecLength = [];
2842 case 'ECOG'
2843 ElectrodeConfig.Type = 'ecog';
2844 ElectrodeConfig.ContactDiameter = 0.004;
2845 ElectrodeConfig.ContactLength = 0.001;
2846 ElectrodeConfig.ElecDiameter = 0.0005;
2847 ElectrodeConfig.ElecLength = [];
2848 case {'SEEG','ECOG+SEEG'}
2849 ElectrodeConfig.Type = 'seeg';
2850 ElectrodeConfig.ContactDiameter = 0.0008;
2851 ElectrodeConfig.ContactLength = 0.002;
2852 ElectrodeConfig.ElecDiameter = 0.0007;
2853 ElectrodeConfig.ElecLength = 0.070;
2854 end
2855 argout1 = ElectrodeConfig;
2856 end
2857
2858 case 'UseSigProcToolbox'
2859 % In a parfor loop: GlobalData is empty => Check only if the toolbox is installed (ignore user preferences)
2860 if isempty(GlobalData) || ~isfield(GlobalData, 'Program') || ~isfield(GlobalData.Program, 'HasSigProcToolbox')
2861 argout1 = exist('fir2', 'file');
2862 else
2863 % Save the result of the check for the SigProc tb
2864 if isempty(GlobalData.Program.HasSigProcToolbox)
2865 % Check if Signal Processing Toolbox is installed
2866 GlobalData.Program.HasSigProcToolbox = (exist('fir2', 'file') == 2);
2867 end
2868 % Return user preferences
2869 if ~GlobalData.Program.HasSigProcToolbox
2870 argout1 = 0;
2871 elseif isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'UseSigProcToolbox')
2872 argout1 = GlobalData.Preferences.UseSigProcToolbox;
2873 else
2874 argout1 = 1;
2875 end
2876 end
2877
2878 case 'CustomColormaps'
2879 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'CustomColormaps') && ~isempty(GlobalData.Preferences.CustomColormaps)
2880 argout1 = GlobalData.Preferences.CustomColormaps;
2881 else
2882 argout1 = repmat(struct('Name', '', 'CMap', []), 0);
2883 end
2884
2885 case 'BFSProperties'
2886 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'BFSProperties') && ~isempty(GlobalData.Preferences.BFSProperties)
2887 argout1 = GlobalData.Preferences.BFSProperties;
2888 else
2889 argout1 = [.33 .0042 .33 .88 .93];
2890 end
2891
2892 case 'LastUsedDirs'
2893 defPref = struct(...
2894 'ImportData', '', ...
2895 'ImportChannel', '', ...
2896 'ImportAnat', '', ...
2897 'ImportMontage', '', ...
2898 'ExportChannel', '', ...
2899 'ExportData', '', ...
2900 'ExportAnat', '', ...
2901 'ExportProtocol', '', ...
2902 'ExportImage', '', ...
2903 'ExportScript', '', ...
2904 'ExportMontage', '');
2905 argout1 = FillMissingFields(contextName, defPref);
2906 % Check that all folders are valid
2907 fields = fieldnames(argout1);
2908 for i = 1:length(fields)
2909 if ~ischar(argout1.(fields{i})) || ~file_exist(argout1.(fields{i}))
2910 argout1.(fields{i}) = '';
2911 end
2912 end
2913
2914 case 'DefaultFormats'
2915 defPref = struct(...
2916 'AnatIn', 'FreeSurfer', ...
2917 'ChannelIn', '', ...
2918 'ChannelOut', '', ...
2919 'DataIn', 'CTF', ...
2920 'DataOut', '', ...
2921 'DipolesIn', '', ...
2922 'DipolesOut', '', ...
2923 'ImageOut', '', ...
2924 'EventsIn', '', ...
2925 'EventsOut', '', ...
2926 'MriIn', '', ...
2927 'MriOut', 'Nifti1', ...
2928 'NoiseCovIn', '', ...
2929 'NoiseCovOut', '', ...
2930 'ResultsIn', '', ...
2931 'ResultsOut', '', ...
2932 'SpmOut', '', ...
2933 'SspIn', '', ...
2934 'SspOut', '', ...
2935 'SurfaceIn', '', ...
2936 'SurfaceOut', '', ...
2937 'LabelIn', '', ...
2938 'LabelOut', '', ...
2939 'TimefreqIn', '', ...
2940 'TimefreqOut', '', ...
2941 'MatrixIn', '', ...
2942 'MatrixOut', '', ...
2943 'MontageIn', '', ...
2944 'MontageOut', '', ...
2945 'FibersIn', '');
2946 argout1 = FillMissingFields(contextName, defPref);
2947
2948 case 'OsType'
2949 switch (mexext)
2950 case 'mexglx', argout1 = 'linux32';
2951 case 'mexa64', argout1 = 'linux64';
2952 case 'mexmaci', argout1 = 'mac32';
2953 case 'mexmaci64', argout1 = 'mac64';
2954 case 'mexs64', argout1 = 'sol64';
2955 case 'mexw32', argout1 = 'win32';
2956 case 'mexw64', argout1 = 'win64';
2957 otherwise, error('Unsupported extension.');
2958 end
2959 % CALL: bst_get('OsType', isMatlab=0)
2960 if (nargin >= 2) && isequal(varargin{2}, 0)
2961 if strcmpi(argout1, 'win32') && (~isempty(strfind(java.lang.System.getProperty('java.home'), '(x86)')) || ~isempty(strfind(java.lang.System.getenv('ProgramFiles(x86)'), '(x86)')))
2962 argout1 = 'win64';
2963 end
2964 end
2965
2966 case 'ImportDataOptions'
2967 defPref = db_template('ImportOptions');
2968 argout1 = FillMissingFields(contextName, defPref);
2969
2970 case 'RawViewerOptions'
2971 defPref = struct(...
2972 'PageDuration', 3, ...
2973 'RemoveBaseline', 'all', ...
2974 'UseCtfComp', 1, ...
2975 'Shortcuts', []);
2976 defPref.Shortcuts = {...
2977 '1', 'event1', 'simple', []; ... % Key, event name, event type (simple,extended,page), epoch time
2978 '2', 'event2', 'simple', []; ...
2979 '3', 'event3', 'simple', []; ...
2980 '4', 'event4', 'simple', []; ...
2981 '5', 'event5', 'simple', []; ...
2982 '6', 'event6', 'simple', []; ...
2983 '7', 'event7', 'simple', []; ...
2984 '8', 'event8', 'simple', []; ...
2985 '9', 'event9', 'simple', []};
2986 argout1 = FillMissingFields(contextName, defPref);
2987 % If invalid PageDuration: reset to default
2988 if (argout1.PageDuration <= 0.1)
2989 argout1.PageDuration = defPref.PageDuration;
2990 end
2991 % If old shortcuts: reset to defaults
2992 if any(size(argout1.Shortcuts) ~= size(defPref.Shortcuts))
2993 disp('BST> Warning: Reset keyboard shortcuts to include new options.');
2994 argout1.Shortcuts = defPref.Shortcuts;
2995 bst_set('RawViewerOptions', argout1);
2996 end
2997
2998 case 'MontageOptions'
2999 defPref = struct('Shortcuts', []);
3000 defPref.Shortcuts = {
3001 %'a', []; ... Note: A is reserved for All channels
3002 'b', []; ...
3003 'c', []; ...
3004 'd', []; ...
3005 'e', []; ...
3006 'f', []; ...
3007 'g', []; ...
3008 'h', []; ...
3009 'i', []; ...
3010 'j', []; ...
3011 'k', []; ...
3012 'l', []; ...
3013 'm', []; ...
3014 'n', []; ...
3015 'o', []; ...
3016 'p', []; ...
3017 'q', []; ...
3018 'r', []; ...
3019 's', []; ...
3020 't', []; ...
3021 'u', []; ...
3022 'v', []; ...
3023 'w', []; ...
3024 'x', []; ...
3025 'y', []; ...
3026 'z', []; ...
3027 };
3028 argout1 = FillMissingFields(contextName, defPref);
3029
3030 case 'TopoLayoutOptions'
3031 defPref = struct(...
3032 'TimeWindow', [], ...
3033 'WhiteBackground', 0, ...
3034 'ShowRefLines', 1, ...
3035 'ShowLegend', 1, ...
3036 'FlipYAxis', 0, ...
3037 'ContourLines', 10);
3038 argout1 = FillMissingFields(contextName, defPref);
3039
3040 case 'StatThreshOptions'
3041 defPref = struct(...
3042 'pThreshold', .05, ...
3043 'durThreshold', 0, ...
3044 'Correction', 'fdr', ...
3045 'Control', [1 2 3]);
3046 argout1 = FillMissingFields(contextName, defPref);
3047 % Make sure that Control is not a string (previous brainstorm version)
3048 if ischar(argout1.Control)
3049 argout1.Control = defPref.Control;
3050 end
3051 % Make sure that 'no' is used instead of 'none' (previous brainstorm version)
3052 if strcmpi(argout1.Correction, 'none')
3053 argout1.Correction = 'no';
3054 end
3055
3056 case 'ContactSheetOptions'
3057 defPref = struct(...
3058 'nImages', 20, ...
3059 'TimeRange', [], ...
3060 'SkipVolume', 0.2);
3061 argout1 = FillMissingFields(contextName, defPref);
3062
3063 case 'ProcessOptions'
3064 defPref = struct(...
3065 'SavedParam', struct(), ...
3066 'MaxBlockSize', 100 / 8 * 1024 * 1024, ... % 100Mb
3067 'LastMaxBlockSize', 100 / 8 * 1024 * 1024); % 100Mb
3068 argout1 = FillMissingFields(contextName, defPref);
3069
3070 case 'ImportEegRawOptions'
3071 defPref = struct(...
3072 'isCanceled', 0, ...
3073 'BaselineDuration', 0, ...
3074 'SamplingRate', 1000, ...
3075 'MatrixOrientation', 'channelXtime', ... % {'channelXtime', 'timeXchannel'}
3076 'VoltageUnits', 'V', ... % {'\muV', 'mV', 'V'}
3077 'SkipLines', 0, ...
3078 'nAvg', 1, ...
3079 'isChannelName', 0); % 1 if the first entry contains the channel name
3080 argout1 = FillMissingFields(contextName, defPref);
3081
3082 case 'BugReportOptions'
3083 defPref = struct(...
3084 'isEnabled', 0, ...
3085 'SmtpServer', 'mailhost.chups.jussieu.fr', ...
3086 'UserEmail', '');
3087 argout1 = FillMissingFields(contextName, defPref);
3088
3089 case 'DefaultSurfaceDisplay'
3090 defPref = struct(...
3091 'SurfShowSulci', 1, ...
3092 'SurfSmoothValue', 0, ...
3093 'DataThreshold', 0.5, ...
3094 'SizeThreshold', 1, ...
3095 'DataAlpha', 0);
3096 argout1 = FillMissingFields(contextName, defPref);
3097
3098 case 'MagneticExtrapOptions'
3099 defPref = struct(...
3100 'ForceWhitening', 0, ...
3101 'EpsilonValue', 0.0001);
3102 argout1 = FillMissingFields(contextName, defPref);
3103
3104 case 'DefaultFreqBands'
3105 argout1 = {...
3106 'delta', '2, 4', 'mean'; ...
3107 'theta', '5, 7', 'mean'; ...
3108 'alpha', '8, 12', 'mean'; ...
3109 'beta', '15, 29', 'mean'; ...
3110 'gamma1', '30, 59', 'mean'; ...
3111 'gamma2', '60, 90', 'mean'};
3112
3113 case 'TimefreqOptions_morlet'
3114 defPref.isTimeBands = 0;
3115 defPref.isFreqBands = 0;
3116 defPref.isFreqLog = 0;
3117 defPref.TimeBands = {};
3118 defPref.Freqs = '1:1:60';
3119 defPref.FreqsLog = '1:40:150';
3120 defPref.FreqBands = bst_get('DefaultFreqBands');
3121 defPref.Measure = 'power';
3122 defPref.SaveKernel = 0;
3123 defPref.Output = 'all';
3124 defPref.RemoveEvoked = 0;
3125 defPref.ClusterFuncTime = 'after';
3126 defPref.MorletFc = 1;
3127 defPref.MorletFwhmTc = 3;
3128 argout1 = FillMissingFields(contextName, defPref);
3129 if isempty(argout1.Freqs)
3130 argout1.Freqs = defPref.Freqs;
3131 end
3132 if ~isempty(argout1.FreqBands) && ((size(argout1.FreqBands,2) ~= 3) || ~all(cellfun(@ischar, argout1.FreqBands(:))) || any(cellfun(@(c)isempty(strtrim(c)), argout1.FreqBands(:))))
3133 argout1.FreqBands = defPref.FreqBands;
3134 end
3135
3136 case 'TimefreqOptions_hilbert'
3137 defPref.isTimeBands = 0;
3138 defPref.isFreqBands = 1;
3139 defPref.isFreqLog = 0;
3140 defPref.TimeBands = {};
3141 defPref.Freqs = [];
3142 defPref.FreqsLog = [];
3143 defPref.FreqBands = bst_get('DefaultFreqBands');
3144 defPref.Measure = 'power';
3145 defPref.SaveKernel = 0;
3146 defPref.Output = 'all';
3147 defPref.RemoveEvoked = 0;
3148 defPref.ClusterFuncTime = 'after';
3149 argout1 = FillMissingFields(contextName, defPref);
3150 if isempty(argout1.Freqs)
3151 argout1.Freqs = defPref.Freqs;
3152 end
3153 if ~isempty(argout1.FreqBands) && (size(argout1.FreqBands,2) == 3) && ~ischar(argout1.FreqBands{1,2})
3154 argout1.FreqBands = defPref.FreqBands;
3155 end
3156
3157 case 'TimefreqOptions_plv'
3158 defPref.isTimeBands = 0;
3159 defPref.isFreqBands = 1;
3160 defPref.isFreqLog = 0;
3161 defPref.TimeBands = {};
3162 defPref.Freqs = [];
3163 defPref.FreqsLog = [];
3164 defPref.FreqBands = bst_get('DefaultFreqBands');
3165 defPref.Measure = 'other';
3166 defPref.SaveKernel = 0;
3167 defPref.Output = 'all';
3168 defPref.ClusterFuncTime = 'after';
3169 argout1 = FillMissingFields(contextName, defPref);
3170 if isempty(argout1.Freqs)
3171 argout1.Freqs = defPref.Freqs;
3172 end
3173 if ~isempty(argout1.FreqBands) && ~ischar(argout1.FreqBands{1,2})
3174 argout1.FreqBands = defPref.FreqBands;
3175 end
3176
3177 case 'TimefreqOptions_fft'
3178 defPref.isTimeBands = 0;
3179 defPref.isFreqBands = 0;
3180 defPref.isFreqLog = 0;
3181 defPref.TimeBands = {};
3182 defPref.Freqs = [];
3183 defPref.FreqsLog = [];
3184 defPref.FreqBands = bst_get('DefaultFreqBands');
3185 defPref.Measure = 'power';
3186 defPref.Output = 'all';
3187 defPref.ClusterFuncTime = 'after';
3188 argout1 = FillMissingFields(contextName, defPref);
3189 if isempty(argout1.Freqs)
3190 argout1.Freqs = defPref.Freqs;
3191 end
3192 if ~isempty(argout1.FreqBands) && ~ischar(argout1.FreqBands{1,2})
3193 argout1.FreqBands = defPref.FreqBands;
3194 end
3195
3196 case 'TimefreqOptions_psd'
3197 defPref.isTimeBands = 0;
3198 defPref.isFreqBands = 0;
3199 defPref.isFreqLog = 0;
3200 defPref.TimeBands = {};
3201 defPref.Freqs = [];
3202 defPref.FreqsLog = [];
3203 defPref.FreqBands = bst_get('DefaultFreqBands');
3204 defPref.Measure = 'power';
3205 defPref.Output = 'all';
3206 defPref.ClusterFuncTime = 'after';
3207 argout1 = FillMissingFields(contextName, defPref);
3208 if isempty(argout1.Freqs)
3209 argout1.Freqs = defPref.Freqs;
3210 end
3211 if ~isempty(argout1.FreqBands) && ~ischar(argout1.FreqBands{1,2})
3212 argout1.FreqBands = defPref.FreqBands;
3213 end
3214
3215 case 'ExportBidsOptions'
3216 defPref.ProjName = [];
3217 defPref.ProjID = [];
3218 defPref.ProjDesc = [];
3219 defPref.Categories = [];
3220 defPref.JsonDataset = ['{' 10 ' "License": "PD"' 10 '}'];
3221 defPref.JsonMeg = ['{' 10 ' "TaskDescription": "My task"' 10 '}'];
3222 argout1 = FillMissingFields(contextName, defPref);
3223
3224 case 'OpenMEEGOptions'
3225 defPref.BemFiles = {};
3226 defPref.BemNames = {'Scalp', 'Skull', 'Brain'};
3227 defPref.BemCond = [1, 0.0125, 1];
3228 defPref.BemSelect = [1 1 1];
3229 defPref.isAdjoint = 0;
3230 defPref.isAdaptative = 1;
3231 defPref.isSplit = 0;
3232 defPref.SplitLength = 4000;
3233 argout1 = FillMissingFields(contextName, defPref);
3234
3235 case 'DuneuroOptions'
3236 defPref = duneuro_defaults();
3237 argout1 = FillMissingFields(contextName, defPref);
3238
3239 case 'GridOptions_dipfit'
3240 defPref = struct(...
3241 'Method', 'isotropic', ...
3242 'nLayers', 17, ...
3243 'Reduction', 3, ...
3244 'nVerticesInit', 4000, ...
3245 'Resolution', 0.020, ...
3246 'FileName', '');
3247 argout1 = FillMissingFields(contextName, defPref);
3248
3249 case 'GridOptions_headmodel'
3250 defPref = struct(...
3251 'Method', 'isotropic', ...
3252 'nLayers', 17, ...
3253 'Reduction', 3, ...
3254 'nVerticesInit', 4000, ...
3255 'Resolution', 0.005, ...
3256 'FileName', '');
3257 argout1 = FillMissingFields(contextName, defPref);
3258
3259 case 'MriOptions'
3260 defPref = struct(...
3261 'isRadioOrient', 0, ...
3262 'isMipAnatomy', 0, ...
3263 'isMipFunctional', 0, ...
3264 'OverlaySmooth', 0, ...
3265 'InterpDownsample', 3, ...
3266 'DistanceThresh', 6, ...
3267 'UpsampleImage', 0, ...
3268 'DefaultAtlas', []);
3269 argout1 = FillMissingFields(contextName, defPref);
3270
3271 case 'DigitizeOptions'
3272 defPref = struct(...
3273 'ComPort', 'COM1', ...
3274 'ComRate', 9600, ...
3275 'ComByteCount', 94, ... % 47 bytes * 2 receivers
3276 'UnitType', 'fastrak', ...
3277 'PatientId', 'S001', ...
3278 'nFidSets', 2, ...
3279 'isBeep', 1, ...
3280 'isMEG', 1, ...
3281 'isSimulate', 0, ...
3282 'Montages', [...
3283 struct('Name', 'No EEG', ...
3284 'Labels', []), ...
3285 struct('Name', 'Default', ...
3286 'Labels', [])], ...
3287 'iMontage', 1);
3288 argout1 = FillMissingFields(contextName, defPref);
3289
3290 case 'ConnectGraphOptions'
3291 % Get interface scaling factor
3292 InterfaceScaling = bst_get('InterfaceScaling');
3293 % Get default values
3294 defPref = struct(...
3295 'LobeFullLabel', 1, ...
3296 'TextDisplayMode', [1 2], ...
3297 'LabelSize', 7 .* InterfaceScaling ./ 100, ...
3298 'NodeSize', 5 .* InterfaceScaling ./ 100, ...
3299 'LinkSize', 1.5 .* InterfaceScaling ./ 100, ...
3300 'BgColor', [0 0 0], ...
3301 'HierarchyNodeIsVisible', 1);
3302 % If we have an additional argument, get the default values
3303 if nargin > 1
3304 argout1 = defPref;
3305 % Otherwise, get the saved values
3306 else
3307 savedValues = FillMissingFields(contextName, defPref);
3308
3309 % if any of the fields are [], replace by default value
3310 % do it here to avoid touching the common FillMissingFields
3311 % function, as other tools may actually want to set [] as desired property
3312 fields = fieldnames(savedValues);
3313 for i=1:numel(fields)
3314 if(isempty(savedValues.(fields{i})))
3315 savedValues.(fields{i}) = defPref.(fields{i});
3316 end
3317 end
3318 argout1 = savedValues;
3319 end
3320
3321 case 'NodelistOptions'
3322 defPref = struct(...
3323 'String', '', ... % What to search for
3324 'Target', 'Comment', ... % What field to search for: {'FileName', 'Comment'}
3325 'Action', 'Select'); % What to do with the filtered files: {'Select', 'Exclude'}
3326 argout1 = FillMissingFields(contextName, defPref);
3327
3328 case 'ReadOnly'
3329 if isfield(GlobalData.DataBase, 'isReadOnly')
3330 argout1 = GlobalData.DataBase.isReadOnly;
3331 else
3332 argout1 = 0;
3333 end
3334
3335 case 'LastPsdDisplayFunction'
3336 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'LastPsdDisplayFunction')
3337 argout1 = GlobalData.Preferences.LastPsdDisplayFunction;
3338 else
3339 argout1 = [];
3340 end
3341
3342 case 'PlotlyCredentials'
3343 try
3344 creds = loadplotlycredentials();
3345 argout1 = creds.username;
3346 argout2 = creds.api_key;
3347 catch
3348 argout1 = '';
3349 argout2 = '';
3350 end
3351
3352 try
3353 config = loadplotlyconfig();
3354 argout3 = config.plotly_domain;
3355 catch
3356 argout3 = '';
3357 end
3358
3359 case 'KlustersExecutable'
3360 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, 'KlustersExecutable')
3361 argout1 = GlobalData.Preferences.KlustersExecutable;
3362 else
3363 argout1 = [];
3364 end
3365
3366
3367 %% ===== FILE FILTERS =====
3368 case 'FileFilters'
3369 switch lower(varargin{2})
3370 case 'mri'
3371 argout1 = {...
3372 {'.img'}, 'MRI: Analyze (*.img/*.hdr)', 'Analyze'; ...
3373 {'.ima'}, 'MRI: BrainVISA GIS (*.ima/*.dim)', 'GIS'; ...
3374 {'.ima'}, 'MRI: BrainVISA GIS (*.ima/*.dim)', 'GIS'; ...
3375 {'.mri'}, 'MRI: CTF (*.mri)', 'CTF'; ...
3376 {'.mat'}, 'MRI: FieldTrip (*.mat)', 'FT-MRI'; ...
3377 {'.mgh','.mgz'}, 'MRI: MGH (*.mgh,*.mgz)', 'MGH'; ...
3378 {'.mnc', '.mni'}, 'MRI: MNI (*.mnc,*.mni)', 'MINC'; ...
3379 {'.nii','.gz'}, 'MRI: NIfTI-1 (*.nii;*.nii.gz)', 'Nifti1'; ...
3380 {'_subjectimage'}, 'MRI: Brainstorm (*subjectimage*.mat)', 'BST'; ...
3381 {'*'}, 'MRI: DICOM (SPM converter)', 'DICOM-SPM'; ...
3382 {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'All MRI files (subject space)', 'ALL'; ...
3383 {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'All MRI files (MNI space)', 'ALL-MNI'; ...
3384 {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'Volume atlas (subject space)', 'ALL-ATLAS'; ...
3385 {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'Volume atlas (MNI space)', 'ALL-MNI-ATLAS'; ...
3386 };
3387 case 'mriout'
3388 argout1 = {...
3389 {'.img'}, 'MRI: Analyze (*.img/*.hdr)', 'Analyze'; ...
3390 {'.ima'}, 'MRI: BrainVISA GIS (*.ima/*.dim)', 'GIS'; ...
3391 {'.mri'}, 'MRI: CTF (*.mri)', 'CTF'; ...
3392 {'.mat'}, 'MRI: FieldTrip (*.mat)', 'FT-MRI'; ...
3393 {'.nii'}, 'MRI: NIfTI-1 (*.nii)', 'Nifti1'...
3394 };
3395 case 'anatin'
3396 argout1 = {...
3397 {'.folder'}, 'FreeSurfer', 'FreeSurfer-fast'; ...
3398 {'.folder'}, 'FreeSurfer + Volume atlases', 'FreeSurfer'; ...
3399 {'.folder'}, 'FreeSurfer + Volume atlases + Thickness', 'FreeSurfer+Thick'; ...
3400 {'.folder'}, 'BrainSuite', 'BrainSuite-fast'; ...
3401 {'.folder'}, 'BrainSuite + Volume atlases', 'BrainSuite'; ...
3402 {'.folder'}, 'BrainVISA', 'BrainVISA'; ...
3403 {'.folder'}, 'CAT12', 'CAT12'; ...
3404 {'.folder'}, 'CAT12 + Thickness', 'CAT12+Thick'; ...
3405 {'.folder'}, 'CIVET', 'CIVET'; ...
3406 {'.folder'}, 'CIVET + Thickness', 'CIVET+Thick'; ...
3407 {'.folder'}, 'HCP MEG/anatomy (pipeline v3)', 'HCPv3'; ...
3408 {'.folder'}, 'SimNIBS', 'SimNIBS'; ...
3409 };
3410 case 'source4d'
3411 argout1 = {...
3412 {'.folder'}, 'NIfTI-1 (*.nii)', 'Nifti1';...
3413 {'.folder'}, 'Analyze (*.img/*.hdr)', 'Analyze'; ...
3414 {'.folder'}, 'Matlab 4D matrix (*voltime*.mat)', 'BST'; ...
3415 };
3416
3417 case 'surface'
3418 argout1 = {...
3419 {'.mesh'}, 'BrainVISA (*.mesh)', 'MESH'; ...
3420 {'_tess', '_head', '_scalp', '_brain', '_cortex', '_innerskull', '_outerskull'}, 'Brainstorm (*.mat)', 'BST'; ...
3421 {'.dfs'}, 'BrainSuite (*.dfs)', 'DFS'; ...
3422 {'.dsgl'}, 'BrainSuite old (*.dsgl)', 'DSGL'; ...
3423 {'.bd0','.bd1','.bd2','.bd3','.bd4','.bd5','.bd6','.bd7','.bd8','.bd9', ...
3424 '.s00','.s01','.s02','.s03','.s04','.s05','.s06','.s07','.s08','.s09'}, ...
3425 'Curry BEM (*.db*;*.s0*)', 'CURRY-BEM';
3426 {'.vtk'}, 'FSL: VTK (*.vtk)', 'VTK'; ...
3427 {'*'}, 'FreeSurfer (*.*)', 'FS';
3428 {'.off'}, 'Geomview OFF (*.off)', 'OFF'; ...
3429 {'.gii'}, 'GIfTI / MRI coordinates (*.gii)', 'GII'; ...
3430 {'.gii'}, 'GIfTI / MNI coordinates (*.gii)', 'GII-MNI'; ...
3431 {'.gii'}, 'GIfTI / World coordinates (*.gii)', 'GII-WORLD'; ...
3432 {'.fif'}, 'MNE (*.fif)', 'FIF'; ...
3433 {'.obj'}, 'MNI OBJ (*.obj)', 'MNIOBJ'; ...
3434 {'.msh'}, 'SimNIBS Gmsh4 (*.msh)', 'SIMNIBS'; ...
3435 {'.tri'}, 'TRI (*.tri)', 'TRI'; ...
3436 {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'Volume mask or atlas (subject space)', 'MRI-MASK'; ...
3437 {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz'}, 'Volume mask or atlas (MNI space)', 'MRI-MASK-MNI'; ...
3438 {'.nwbaux'}, 'Neurodata Without Borders (*.nwbaux)', 'NWB'; ...
3439 {'*'}, 'All surface files (*.*)', 'ALL'; ...
3440 };
3441
3442 case 'surfaceout'
3443 argout1 = {...
3444 {'.mesh'}, 'BrainVISA (*.mesh)', 'MESH'; ...
3445 {'.dfs'}, 'BrainSuite (*.dfs)', 'DFS'; ...
3446 {'.fs'}, 'FreeSurfer (*.fs)', 'FS'
3447 {'.off'}, 'Geomview OFF (*.off)', 'OFF'; ...
3448 {'.gii'}, 'GIfTI (*.gii)', 'GII'; ...
3449 {'.tri'}, 'TRI (*.tri)', 'TRI'; ...
3450 };
3451
3452 case 'data'
3453 argout1 = {...
3454 {'.*'}, 'MEG/EEG: 4D-Neuroimaging/BTi (*.*)', '4D'; ...
3455 {'.meg4','.res4'}, 'MEG/EEG: CTF (*.ds;*.meg4;*.res4)', 'CTF'; ...
3456 {'.fif'}, 'MEG/EEG: Elekta-Neuromag (*.fif)', 'FIF'; ...
3457 {'.mat'}, 'MEG/EEG: FieldTrip (*.mat)', 'FT-TIMELOCK'; ...
3458 {'.raw'}, 'MEG/EEG: ITAB (*.raw)', 'ITAB'; ...
3459 {'.kdf'}, 'MEG/EEG: KRISS MEG (*.kdf)', 'KDF'; ...
3460 {'.mrk','.sqd','.con','.raw','.ave'}, 'MEG/EEG: Ricoh (*.sqd;*.con;*.raw;*.ave;*.mrk)', 'RICOH'; ...
3461 {'.mat'}, 'MEG/EEG: SPM (*.mat/.dat)', 'SPM-DAT'; ...
3462 {'.mrk','.sqd','.con','.raw','.ave'}, 'MEG/EEG: Yokogawa/KIT (*.sqd;*.con;*.raw;*.ave;*.mrk)', 'KIT'; ...
3463 {'.meghdf5'}, 'MEG/EEG: York Instruments MEGSCAN (.meghdf5)', 'MEGSCAN-HDF5'; ...
3464 {'.bst'}, 'MEG/EEG: Brainstorm binary (*.bst)', 'BST-BIN'; ...
3465 {'.adicht'}, 'EEG: ADInstruments LabChart (*.adicht)', 'EEG-ADICHT'; ...
3466 {'.msr'}, 'EEG: ANT ASA (*.msr)', 'EEG-ANT-MSR'; ...
3467 {'.cnt','.avr'}, 'EEG: ANT EEProbe (*.cnt;*.avr)', 'EEG-ANT-CNT'; ...
3468 {'*'}, 'EEG: ASCII text (*.*)', 'EEG-ASCII'; ...
3469 {'.raw'}, 'EEG: Axion AxIS (*.raw)', 'EEG-AXION'; ...
3470 {'.bdf'}, 'EEG: BDF (*.bdf)', 'EEG-BDF'; ...
3471 {'.avr','.mux','.mul'}, 'EEG: BESA exports (*.avr;*.mul;*.mux)', 'EEG-BESA'; ...
3472 {'.ns1','.ns2','.ns3','.ns4','.ns5','.ns6'}, 'EEG: Blackrock NeuroPort (*.nsX/*.nev)', 'EEG-BLACKROCK';
3473 {'.eeg','.dat'}, 'EEG: BrainVision BrainAmp (*.eeg;*.dat)', 'EEG-BRAINAMP'; ...
3474 {'.txt'}, 'EEG: BrainVision Analyzer (*.txt)', 'EEG-BRAINVISION'; ...
3475 {'.sef','.ep','.eph'}, 'EEG: Cartool (*.sef;*.ep;*.eph)', 'EEG-CARTOOL'; ...
3476 {'.dat','.cdt'}, 'EEG: Curry (*.dat;*.cdt)', 'EEG-CURRY'; ...
3477 {'.smr','.son'}, 'EEG: CED Spike2 old 32bit (*.smr;*.son)', 'EEG-SMR'; ...
3478 {'.smr','.smrx'}, 'EEG: CED Spike2 new 64bit (*.smr;*.smrx)', 'EEG-SMRX'; ...
3479 {'.rda'}, 'EEG: Compumedics ProFusion Sleep (*.rda)', 'EEG-COMPUMEDICS-PFS'; ...
3480 {'.bin'}, 'EEG: Deltamed Coherence-Neurofile (*.bin)', 'EEG-DELTAMED'; ...
3481 {'.edf','.rec'}, 'EEG: EDF / EDF+ (*.rec;*.edf)', 'EEG-EDF'; ...
3482 {'.set'}, 'EEG: EEGLAB (*.set)', 'EEG-EEGLAB'; ...
3483 {'.raw'}, 'EEG: EGI Netstation RAW (*.raw)', 'EEG-EGI-RAW'; ...
3484 {'.mff','.bin'}, 'EEG: EGI-Philips (*.mff)', 'EEG-EGI-MFF'; ...
3485 {'.edf'}, 'EEG: EmotivPRO (*.edf)', 'EEG-EMOTIV'; ...
3486 {'.erp','.hdr'}, 'EEG: ERPCenter (*.hdr;*.erp)', 'EEG-ERPCENTER'; ...
3487 {'.erp'}, 'EEG: ERPLab (*.erp)', 'EEG-ERPLAB'; ...
3488 {'.mat','.hdf5'}, 'EEG: g.tec Matlab (*.mat,*.hdf5)', 'EEG-GTEC'; ...
3489 {'.rhd','.rhs'}, 'EEG: Intan (*.rhd,*.rhs)', 'EEG-INTAN'; ...
3490 {'.mb2'}, 'EEG: MANSCAN (*.mb2)', 'EEG-MANSCAN'; ...
3491 {'.trc'}, 'EEG: Micromed (*.trc)', 'EEG-MICROMED'; ...
3492 {'.mat'}, 'EEG: Matlab matrix (*.mat)', 'EEG-MAT'; ...
3493 {'.csv'}, 'EEG: Muse (*.csv)', 'EEG-MUSE-CSV'; ...
3494 {'.ncs'}, 'EEG: Neuralynx (*.ncs)', 'EEG-NEURALYNX'; ...
3495 {'.nwb'}, 'EEG: Neurodata Without Borders (*.nwb)','NWB'; ...
3496 {'.nedf','.easy'}, 'EEG: Neuroelectrics (*.nedf;*.easy)', 'EEG-NEUROELECTRICS'; ...
3497 {'.bin'}, 'EEG: NeurOne session folder', 'EEG-NEURONE'; ...
3498 {'.cnt','.avg','.eeg','.dat'}, 'EEG: Neuroscan (*.cnt;*.eeg;*.avg;*.dat)', 'EEG-NEUROSCAN'; ...
3499 {'.eeg','.dat'}, 'EEG: NeuroScope (*.eeg;*.dat)', 'EEG-NEUROSCOPE'; ...
3500 {'.e'}, 'EEG: Nicolet (*.e)', 'EEG-NICOLET'; ...
3501 {'.eeg'}, 'EEG: Nihon Kohden (*.eeg)', 'EEG-NK'; ...
3502 {'.dat'}, 'EEG: Open Ephys flat binary (*.dat)', 'EEG-OEBIN'; ...
3503 {'.plx','.pl2'}, 'EEG: Plexon (*.plx;*.pl2)', 'EEG-PLEXON'; ...
3504 {'.ns1','.ns2','.ns3','.ns4','.ns5','.ns6'}, 'EEG: Ripple Trellis (*.nsX/*.nev)', 'EEG-RIPPLE'; ...
3505 {'.h5'}, 'EEG: The Virtual Brain (*_TimeSeriesEEG.h5)', 'EEG-TVB'; ...
3506 {'.csv'}, 'EEG: Wearable Sensing (*.csv)', 'EEG-WS-CSV'; ...
3507 {'.nirs'}, 'NIRS: Brainsight (*.nirs)', 'NIRS-BRS'; ...
3508 {'.bnirs','.jnirs','.snirf'}, 'NIRS: SNIRF (*.snirf)', 'NIRS-SNIRF'; ...
3509 {'.edf'}, 'Eye tracker: EyeLink (*.edf)', 'EYELINK'; ...
3510 {'.tsv'}, 'Eye tracker: Tobii glasses (*.tsv)', 'EYE-TOBII-TSV'; ...
3511 };
3512 case 'raw'
3513 argout1 = {...
3514 {'.*'}, 'MEG/EEG: 4D-Neuroimaging/BTi (*.*)', '4D'; ...
3515 {'.meg4','.res4'}, 'MEG/EEG: CTF (*.ds;*.meg4;*.res4)', 'CTF'; ...
3516 {'.fif'}, 'MEG/EEG: Elekta-Neuromag (*.fif)', 'FIF'; ...
3517 {'.mat'}, 'MEG/EEG: FieldTrip (*.mat)', 'FT-TIMELOCK'; ...
3518 {'.raw'}, 'MEG/EEG: ITAB (*.raw)', 'ITAB'; ...
3519 {'.kdf'}, 'MEG/EEG: KRISS MEG (*.kdf)', 'KDF'; ...
3520 {'.mrk','.sqd','.con','.raw','.ave'}, 'MEG/EEG: Ricoh (*.sqd;*.con;*.raw;*.ave;*.mrk)', 'RICOH'; ...
3521 {'.mat'}, 'MEG/EEG: SPM (*.mat/.dat)', 'SPM-DAT'; ...
3522 {'.mrk','.sqd','.con','.raw','.ave'}, 'MEG/EEG: Yokogawa/KIT (*.sqd;*.con;*.raw;*.ave;*.mrk)', 'KIT'; ...
3523 {'.meghdf5'}, 'MEG/EEG: York Instruments MEGSCAN (.meghdf5)', 'MEGSCAN-HDF5'; ...
3524 {'.bst'}, 'MEG/EEG: Brainstorm binary (*.bst)', 'BST-BIN'; ...
3525 {'.adicht'}, 'EEG: ADInstruments LabChart (*.adicht)', 'EEG-ADICHT'; ...
3526 {'.msr'}, 'EEG: ANT ASA (*.msr)', 'EEG-ANT-MSR'; ...
3527 {'.cnt','.avr'}, 'EEG: ANT EEProbe (*.cnt;*.avr)', 'EEG-ANT-CNT'; ...
3528 {'*'}, 'EEG: ASCII text (*.*)', 'EEG-ASCII'; ...
3529 {'.raw'}, 'EEG: Axion AxIS (*.raw)', 'EEG-AXION'; ...
3530 {'.bdf'}, 'EEG: BDF (*.bdf)', 'EEG-BDF'; ...
3531 {'.avr','.mux','.mul'}, 'EEG: BESA exports (*.avr;*.mul;*.mux)', 'EEG-BESA'; ...
3532 {'.ns1','.ns2','.ns3','.ns4','.ns5','.ns6'}, 'EEG: Blackrock NeuroPort (*.nsX/*.nev)', 'EEG-BLACKROCK';
3533 {'.eeg','.dat'}, 'EEG: BrainVision BrainAmp (*.eeg;*.dat)', 'EEG-BRAINAMP'; ...
3534 {'.txt'}, 'EEG: BrainVision Analyzer (*.txt)', 'EEG-BRAINVISION'; ...
3535 {'.sef','.ep','.eph'}, 'EEG: Cartool (*.sef;*.ep;*.eph)', 'EEG-CARTOOL'; ...
3536 {'.smr','.son'}, 'EEG: CED Spike2 old 32bit (*.smr;*.son)', 'EEG-SMR'; ...
3537 {'.smr','.smrx'}, 'EEG: CED Spike2 new 64bit (*.smr;*.smrx)', 'EEG-SMRX'; ...
3538 {'.rda'}, 'EEG: Compumedics ProFusion Sleep (*.rda)', 'EEG-COMPUMEDICS-PFS'; ...
3539 {'.dat','.cdt'}, 'EEG: Curry (*.dat;*.cdt)', 'EEG-CURRY'; ...
3540 {'.bin'}, 'EEG: Deltamed Coherence-Neurofile (*.bin)', 'EEG-DELTAMED'; ...
3541 {'.edf','.rec'}, 'EEG: EDF / EDF+ (*.rec;*.edf)', 'EEG-EDF'; ...
3542 {'.set'}, 'EEG: EEGLAB (*.set)', 'EEG-EEGLAB'; ...
3543 {'.raw'}, 'EEG: EGI Netstation RAW (*.raw)', 'EEG-EGI-RAW'; ...
3544 {'.mff','.bin'}, 'EEG: EGI-Philips (*.mff)', 'EEG-EGI-MFF'; ...
3545 {'.edf'}, 'EEG: EmotivPRO (*.edf)', 'EEG-EMOTIV'; ...
3546 {'.mat','.hdf5'}, 'EEG: g.tec Matlab (*.mat,*.hdf5)', 'EEG-GTEC'; ...
3547 {'.rhd','.rhs'}, 'EEG: Intan (*.rhd,*.rhs)', 'EEG-INTAN'; ...
3548 {'.mb2'}, 'EEG: MANSCAN (*.mb2)', 'EEG-MANSCAN'; ...
3549 {'.mat'}, 'EEG: Matlab matrix (*.mat)', 'EEG-MAT'; ...
3550 {'.csv'}, 'EEG: Muse (*.csv)', 'EEG-MUSE-CSV'; ...
3551 {'.trc'}, 'EEG: Micromed (*.trc)', 'EEG-MICROMED'; ...
3552 {'.ncs'}, 'EEG: Neuralynx (*.ncs)', 'EEG-NEURALYNX'; ...
3553 {'.nwb'}, 'EEG: Neurodata Without Borders (*.nwb)','NWB'; ...
3554 {'.nedf','.easy'}, 'EEG: Neuroelectrics (*.nedf;*.easy)', 'EEG-NEUROELECTRICS'; ...
3555 {'.bin'}, 'EEG: NeurOne session folder', 'EEG-NEURONE'; ...
3556 {'.cnt','.avg','.eeg','.dat'}, 'EEG: Neuroscan (*.cnt;*.eeg;*.avg;*.dat)', 'EEG-NEUROSCAN'; ...
3557 {'.eeg','.dat'}, 'EEG: NeuroScope (*.eeg;*.dat)', 'EEG-NEUROSCOPE'; ...
3558 {'.e'}, 'EEG: Nicolet (*.e)', 'EEG-NICOLET'; ...
3559 {'.eeg'}, 'EEG: Nihon Kohden (*.eeg)', 'EEG-NK'; ...
3560 {'.dat'}, 'EEG: Open Ephys flat binary (*.dat)', 'EEG-OEBIN'; ...
3561 {'.plx','.pl2'}, 'EEG: Plexon (*.plx;.pl2)' 'EEG-PLEXON'; ...
3562 {'.ns1','.ns2','.ns3','.ns4','.ns5','.ns6'}, 'EEG: Ripple Trellis (*.nsX/*.nev)', 'EEG-RIPPLE'; ...
3563 {'.h5'}, 'EEG: The Virtual Brain (*_TimeSeriesEEG.h5)', 'EEG-TVB'; ...
3564 {'.tbk'}, 'EEG: Tucker Davis Technologies (*.tbk)', 'EEG-TDT'; ...
3565 {'.csv'}, 'EEG: Wearable Sensing (*.csv)', 'EEG-WS-CSV'; ...
3566 {'.trc','.eeg','.e','.bin','.rda','.edf','.bdf'}, 'SEEG: Deltamed/Micromed/NK/Nicolet/BrainVision/EDF', 'SEEG-ALL'; ...
3567 {'.trc','.eeg','.e','.bin','.rda','.edf','.bdf'}, 'ECOG: Deltamed/Micromed/NK/Nicolet/BrainVision/EDF', 'ECOG-ALL'; ...
3568 {'.nirs'}, 'NIRS: Brainsight (*.nirs)', 'NIRS-BRS'; ...
3569 {'.bnirs','.jnirs','.snirf'}, 'NIRS: SNIRF (*.snirf)', 'NIRS-SNIRF'; ...
3570 {'.edf'}, 'Eye tracker: EyeLink (*.edf)', 'EYELINK'; ...
3571 {'.tsv'}, 'Eye tracker: Tobii glasses (*.tsv)', 'EYE-TOBII-TSV'; ...
3572 };
3573
3574 case 'dataout'
3575 argout1 = {...
3576 {'.bst'}, 'MEG/EEG: Brainstorm binary (*.bst)', 'BST-BIN'; ...
3577 {'.mat'}, 'MEG/EEG: FieldTrip timelock (*.mat)', 'FT-TIMELOCK'; ...
3578 {'.mat'}, 'MEG/EEG: SPM (*.mat/.dat)', 'SPM-DAT'; ...
3579 {'.eeg'}, 'EEG: BrainVision BrainAmp (*.eeg)', 'EEG-BRAINAMP'; ...
3580 {'.eph'}, 'EEG: Cartool EPH (*.eph)', 'EEG-CARTOOL-EPH'; ...
3581 {'.raw'}, 'EEG: EGI NetStation RAW (*.raw)', 'EEG-EGI-RAW'; ...
3582 {'.edf'}, 'EEG: European Data Format (*.edf)', 'EEG-EDF'; ...
3583 {'.snirf'}, 'NIRS: SNIRF (*.snirf)', 'NIRS-SNIRF'; ...
3584 {'.txt'}, 'ASCII: Space-separated, fixed column size (*.txt)', 'ASCII-SPC'; ...
3585 {'.txt'}, 'ASCII: Space-separated with header, fixed column size (*.txt)', 'ASCII-SPC-HDR'; ...
3586 {'.tsv'}, 'ASCII: Tab-separated (*.tsv)', 'ASCII-TSV'; ...
3587 {'.tsv'}, 'ASCII: Tab-separated with header (*.tsv)', 'ASCII-TSV-HDR'; ...
3588 {'.tsv'}, 'ASCII: Tab-separated with header transposed (*.tsv)', 'ASCII-TSV-HDR-TR'; ...
3589 {'.csv'}, 'ASCII: Comma-separated (*.csv)', 'ASCII-CSV'; ...
3590 {'.csv'}, 'ASCII: Comma-separated with header (*.csv)', 'ASCII-CSV-HDR'; ...
3591 {'.csv'}, 'ASCII: Comma-separated with header transposed (*.csv)', 'ASCII-CSV-HDR-TR'; ...
3592 {'.xlsx'}, 'Microsoft Excel (*.xlsx)', 'EXCEL'; ...
3593 {'.xlsx'}, 'Microsoft Excel transposed (*.xlsx)', 'EXCEL-TR'; ...
3594 {'_timeseries'}, 'Brainstorm matrix (*timeseries*.mat)', 'BST'; ...
3595 };
3596 case 'rawout'
3597 argout1 = {...
3598 {'.bst'}, 'MEG/EEG: Brainstorm binary (*.bst)', 'BST-BIN'; ...
3599 {'.mat'}, 'MEG/EEG: SPM (*.mat/.dat)', 'SPM-DAT'; ...
3600 {'.eeg'}, 'EEG: BrainVision BrainAmp (*.eeg)', 'EEG-BRAINAMP'; ...
3601 {'.raw'}, 'EEG: EGI NetStation RAW (*.raw)', 'EEG-EGI-RAW'; ...
3602 {'.edf'}, 'EEG: European Data Format (*.edf)', 'EEG-EDF'; ...
3603 {'.snirf'}, 'NIRS: SNIRF (*.snirf)', 'NIRS-SNIRF'; ...
3604 };
3605 case 'events'
3606 argout1 = {...
3607 {'.trg'}, 'ANT EEProbe (*.trg)', 'ANT'; ...
3608 {'.mrk'}, 'AnyWave (*.mrk)', 'ANYWAVE'; ...
3609 {'.evt'}, 'BESA (*.evt)', 'BESA'; ...
3610 {'.tsv'}, 'BIDS events: onset, duration, trial_type, channel (*.tsv)', 'BIDS'; ...
3611 {'.vmrk'}, 'BrainVision BrainAmp (*.vmrk)', 'BRAINAMP'; ...
3612 {'_events'}, 'Brainstorm (events*.mat)', 'BST'; ...
3613 {'.mrk'}, 'Cartool (*.mrk)', 'CARTOOL'; ...
3614 {'.mrk'}, 'CTF MarkerFile (*.mrk)', 'CTF'; ...
3615 {'.cef'}, 'Curry (*.cef)', 'CURRY'; ...
3616 {'.eve','.fif'}, 'Elekta-Neuromag MNE (*.eve;*.fif)', 'FIF'; ...
3617 {'.evl','.txt'}, 'Elekta-Neuromag Graph (*.evl;*.txt)', 'GRAPH'; ...
3618 {'.txt','.mat'}, 'FieldTrip trial definition (*.txt;*.mat)', 'TRL'; ...
3619 {'.trg'}, 'KRISS MEG (*.trg)', 'KDF'; ...
3620 {'.evt'}, 'Micromed (*.evt)', 'MICROMED'; ...
3621 {'.ev2'}, 'Neuroscan (*.ev2)', 'NEUROSCAN'; ...
3622 {'.txt'}, 'Nicolet export (*.txt)', 'NICOLET'; ...
3623 {'timestamps.npy'},'Open Ephys (timestamps.npy)', 'OEBIN'; ...
3624 {'.log'}, 'Presentation (*.log)', 'PRESENTATION'; ...
3625 {'.mrk','.sqd','.con','.raw','.ave'}, 'Ricoh (*.mrk;*.sqd;*.con;*.raw;*.ave)', 'RICOH'; ...
3626 {'.txt'}, 'XLTEK export (*.txt)', 'XLTEK'; ...
3627 {'.mrk','.sqd','.con','.raw','.ave'}, 'Yokogawa/KIT (*.mrk;*.sqd;*.con;*.raw;*.ave)', 'KIT'; ...
3628 {'.*'}, 'Array of times (*.mat;*.*)', 'ARRAY-TIMES'; ...
3629 {'.*'}, 'Array of samples (*.mat;*.*)', 'ARRAY-SAMPLES'; ...
3630 {'.txt','.csv'}, 'CSV text file: label, time, duration (*.txt;*.csv)', 'CSV-TIME'; ...
3631 {'.*'}, 'CTF Video Times (.txt)', 'CTFVIDEO'; ...
3632 };
3633 case 'eventsout'
3634 argout1 = {...
3635 {'.mrk'}, 'AnyWave (*.mrk)', 'ANYWAVE'; ...
3636 {'_events'}, 'Brainstorm (events*.mat)', 'BST'; ...
3637 {'.vmrk'}, 'BrainVision BrainAmp (*.vmrk)', 'BRAINAMP'; ...
3638 {'.mrk'}, 'CTF MarkerFile (*.mrk)', 'CTF'; ...
3639 {'.eve','.fif'}, 'Elekta-Neuromag/MNE (*.eve)', 'FIF'; ...
3640 {'.evl'}, 'Elekta-Neuromag Graph (Alternative Style) (*.evl)', 'GRAPH_ALT'; ...
3641 {'.txt'}, 'Array of times (*.txt)', 'ARRAY-TIMES'; ...
3642 {'.txt'}, 'Array of samples (*.txt)', 'ARRAY-SAMPLES'; ...
3643 {'.txt','.csv'}, 'CSV text file: label, time, duration (*.txt;*.csv)', 'CSV-TIME'; ...
3644 {'.txt'}, 'CTF Video Times (*.txt)', 'CTFVIDEO'; ...
3645 };
3646 case 'channel'
3647 argout1 = {...
3648 {'.*'}, 'MEG/EEG: 4D-Neuroimaging/BTi (*.*)', '4D'; ...
3649 {'.meg4','.res4'}, 'MEG/EEG: CTF (*.ds;*.meg4;*.res4)', 'CTF' ; ...
3650 {'.fif'}, 'MEG/EEG: Elekta-Neuromag (*.fif)', 'FIF'; ...
3651 {'.kdf'}, 'MEG/EEG: KRISS MEG (*.kdf)', 'KDF'; ...
3652 {'.raw'}, 'MEG/EEG: ITAB (*.raw)', 'ITAB'; ...
3653 {'.mrk','.sqd','.con','.raw','.ave'}, 'MEG/EEG: Ricoh (*.sqd;*.con;*.raw;*.ave;*.mrk)', 'RICOH'; ...
3654 {'.mrk','.sqd','.con','.raw','.ave'}, 'MEG/EEG: Yokogawa/KIT (*.sqd;*.con;*.raw;*.ave;*.mrk)', 'KIT'; ...
3655 {'.meghdf5'}, 'MEG/EEG: York Instruments MEGSCAN (.meghdf5)', 'MEGSCAN-HDF5'; ...
3656 {'.bst'}, 'MEG/EEG: Brainstorm binary (*.bst)', 'BST-BIN'; ...
3657 {'_channel'}, 'MEG/EEG: Brainstorm (channel*.mat)', 'BST'; ...
3658 {'.elc'}, 'EEG: ANT ASA/Xensor (*.elc)', 'XENSOR'; ...
3659 {'.sfp','.elp','.ela','.eps'}, 'EEG: BESA (*.sfp;*.elp;*.eps/*.ela)', 'BESA'; ...
3660 {'.bvef','.bvct','.txt'}, 'EEG: BrainVision electrode file (*.bvef,*.bvct,*.txt)', 'BRAINVISION'; ...
3661 {'.tsv'}, 'EEG: BIDS electrodes.tsv, subject space mm (*.tsv)', 'BIDS-OTHER-MM'; ...
3662 {'.tsv'}, 'EEG: BIDS electrodes.tsv, MNI space mm (*.tsv)', 'BIDS-MNI-MM'; ...
3663 {'.els','.xyz'}, 'EEG: Cartool (*.els;*.xyz)', 'CARTOOL'; ...
3664 {'.eeg'}, 'EEG: MegDraw (*.eeg)', 'MEGDRAW'; ...
3665 {'.res','.rs3','.pom'}, 'EEG: Curry (*.res;*.rs3;*.pom)', 'CURRY'; ...
3666 {'.ced','.xyz','.set'}, 'EEG: EEGLAB (*.ced;*.xyz;*.set)', 'EEGLAB'; ...
3667 {'.elc'}, 'EEG: EETrak (*.elc)', 'EETRAK'; ...
3668 {'.sfp'}, 'EEG: EGI (*.sfp)', 'EGI'; ...
3669 {'coordinates.xml'}, 'EEG: EGI-Philips (coordinates.xml)', 'MFF'; ...
3670 {'.elp'}, 'EEG: EMSE (*.elp)', 'EMSE'; ...
3671 {'.pts','.csv'}, 'EEG: IntrAnat, subject space (*.pts;*.csv)', 'INTRANAT'; ...
3672 {'.pts','.csv'}, 'EEG: IntrAnat, MNI space (*.pts;*.csv)', 'INTRANAT_MNI'; ...
3673 {'.csv'}, 'EEG: Localite (*.csv)', 'LOCALITE'; ...
3674 {'.dat','.tri','.txt','.asc'}, 'EEG: Neuroscan (*.dat;*.tri;*.txt;*.asc)', 'NEUROSCAN'; ...
3675 {'.pos','.pol','.elp','.txt'}, 'EEG: Polhemus (*.pos;*.pol;*.elp;*.txt)', 'POLHEMUS'; ...
3676 {'.csv'}, 'EEG: SimNIBS (*.csv)', 'SIMNIBS'; ...
3677 {'.h5'}, 'EEG: The Virtual Brain (*_SensorsEEG.h5)', 'TVB'; ...
3678 {'*'}, 'EEG: ASCII: Name,XYZ (*.*)', 'ASCII_NXYZ'; ...
3679 {'*'}, 'EEG: ASCII: Name,XYZ_MNI (*.*)', 'ASCII_NXYZ_MNI'; ...
3680 {'*'}, 'EEG: ASCII: Name,XYZ_World (*.*)', 'ASCII_NXYZ_WORLD'; ...
3681 {'*'}, 'EEG: ASCII: Name,XY (*.*)', 'ASCII_NXY'; ...
3682 {'*'}, 'EEG: ASCII: XYZ (*.*)', 'ASCII_XYZ'; ...
3683 {'*'}, 'EEG: ASCII: XYZ_MNI (*.*)', 'ASCII_XYZ_MNI'; ...
3684 {'*'}, 'EEG: ASCII: XYZ_World (*.*)', 'ASCII_XYZ_WORLD'; ...
3685 {'*'}, 'EEG: ASCII: XY (*.*)', 'ASCII_XY'; ...
3686 {'*'}, 'EEG: ASCII: XYZ,Name (*.*)', 'ASCII_XYZN'; ...
3687 {'*'}, 'EEG: ASCII: XYZ_MNI,Name (*.*)', 'ASCII_XYZN_MNI'; ...
3688 {'*'}, 'EEG: ASCII: XYZ_World,Name (*.*)', 'ASCII_XYZN_WORLD'; ...
3689 {'*'}, 'EEG: ASCII: Name,Theta,Phi (*.*)', 'ASCII_NTP'; ...
3690 {'*'}, 'EEG: ASCII: Theta,Phi (*.*)', 'ASCII_TP'; ...
3691 };
3692 case 'channelout'
3693 argout1 = {...
3694 {'.pos'}, 'EEG+Headshape: Polhemus (*.pos)', 'POLHEMUS'; ...
3695 {'.eeg'}, 'Headshape: MegDraw (*.eeg)', 'MEGDRAW'; ...
3696 {'.pos'}, 'Headshape: Polhemus (*.pos)', 'POLHEMUS-HS'; ...
3697 {'.txt'}, 'Headshape: ASCII: XYZ (*.txt)', 'ASCII_XYZ-HS'; ...
3698 {'.txt'}, 'Headshape: ASCII: XYZ_World (*.txt)', 'ASCII_XYZ_WORLD-HS'; ...
3699 {'.txt'}, 'Headshape: ASCII: Name,XYZ (*.txt)', 'ASCII_NXYZ-HS'; ...
3700 {'.txt'}, 'Headshape: ASCII: Name,XYZ_World (*.txt)', 'ASCII_NXYZ_WORLD-HS'; ...
3701 {'.txt'}, 'Headshape: ASCII: XYZ,Name (*.txt)', 'ASCII_XYZN-HS'; ...
3702 {'.txt'}, 'Headshape: ASCII: XYZ_World,Name (*.txt)', 'ASCII_XYZN_WORLD-HS'; ...
3703 {'.sfp'}, 'EEG: BESA (*.sfp)', 'BESA-SFP'; ...
3704 {'.elp'}, 'EEG: BESA (*.elp)', 'BESA-ELP'; ...
3705 {'.xyz'}, 'EEG: Cartool (*.xyz)', 'CARTOOL-XYZ'; ...
3706 {'.res'}, 'EEG: Curry (*.res)', 'CURRY-RES'; ...
3707 {'.xyz'}, 'EEG: EEGLAB (*.xyz)', 'EEGLAB-XYZ'; ...
3708 {'.sfp'}, 'EEG: EGI (*.sfp)', 'EGI'; ...
3709 {'.txt'}, 'EEG: ASCII: XYZ (*.txt)', 'ASCII_XYZ-EEG'; ...
3710 {'.txt'}, 'EEG: ASCII: XYZ_MNI (*.txt)', 'ASCII_XYZ_MNI-EEG'; ...
3711 {'.txt'}, 'EEG: ASCII: XYZ_World (*.txt)', 'ASCII_XYZ_WORLD-EEG'; ...
3712 {'.txt'}, 'EEG: ASCII: Name,XYZ (*.txt)', 'ASCII_NXYZ-EEG'; ...
3713 {'.txt'}, 'EEG: ASCII: Name,XYZ_MNI (*.txt)', 'ASCII_NXYZ_MNI-EEG'; ...
3714 {'.txt'}, 'EEG: ASCII: Name,XYZ_World (*.txt)', 'ASCII_NXYZ_WORLD-EEG'; ...
3715 {'.txt'}, 'EEG: ASCII: XYZ,Name (*.txt)', 'ASCII_XYZN-EEG'; ...
3716 {'.txt'}, 'EEG: ASCII: XYZ_MNI,Name (*.txt)', 'ASCII_XYZN_MNI-EEG'; ...
3717 {'.txt'}, 'EEG: ASCII: XYZ_World,Name (*.txt)', 'ASCII_XYZN_WORLD-EEG'; ...
3718 {'.txt'}, 'NIRS: Brainsight (*.txt)', 'BRAINSIGHT-TXT'; ...
3719 };
3720 case 'labelin'
3721 argout1 = {...
3722 {'.dfs'}, 'BrainSuite atlas (*.dfs)', 'DFS'; ...
3723 {'.annot'}, 'FreeSurfer atlas (*.annot)', 'FS-ANNOT'; ...
3724 {'.label'}, 'FreeSurfer ROI, single scout (*.label)', 'FS-LABEL-SINGLE'; ...
3725 {'.label'}, 'FreeSurfer ROI, probability map (*.label)', 'FS-LABEL'; ...
3726 {'.gii'}, 'GIfTI texture (*.gii)', 'GII-TEX'; ...
3727 {'.dset'}, 'SUMA atlas (*.dset)', 'DSET'; ...
3728 {'_scout'}, 'Brainstorm scouts (*scout*.mat)', 'BST'; ...
3729 {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'Volume mask or atlas (dilated, subject space)', 'MRI-MASK'; ...
3730 {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz'}, 'Volume mask or atlas (dilated, MNI space)', 'MRI-MASK-MNI'; ...
3731 {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'Volume mask or atlas (no overlap, subject space)', 'MRI-MASK-NOOVERLAP'; ...
3732 {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz'}, 'Volume mask or atlas (no overlap, MNI space)', 'MRI-MASK-NOOVERLAP-MNI'; ...
3733 };
3734 case 'resultsout'
3735 argout1 = {...
3736 {'_sources'}, 'Brainstorm sources (*sources*.mat)', 'BST'; ...
3737 {'.mat'}, 'FieldTrip sources (*.mat)', 'FT-SOURCES'; ...
3738 {'.txt'}, 'ASCII: Space-separated, fixed columns size (*.txt)', 'ASCII-SPC'; ...
3739 {'.txt'}, 'ASCII: Space-separated with header, fixed column size (*.txt)', 'ASCII-SPC-HDR'; ...
3740 {'.tsv'}, 'ASCII: Tab-separated (*.tsv)', 'ASCII-TSV'; ...
3741 {'.tsv'}, 'ASCII: Tab-separated with header (*.tsv)', 'ASCII-TSV-HDR'; ...
3742 {'.tsv'}, 'ASCII: Tab-separated with header transposed (*.tsv)', 'ASCII-TSV-HDR-TR'; ...
3743 {'.csv'}, 'ASCII: Comma-separated (*.csv)', 'ASCII-CSV'; ...
3744 {'.csv'}, 'ASCII: Comma-separated with header (*.csv)', 'ASCII-CSV-HDR'; ...
3745 {'.csv'}, 'ASCII: Comma-separated with header transposed (*.csv)', 'ASCII-CSV-HDR-TR'; ...
3746 {'.xlsx'}, 'Microsoft Excel (*.xlsx)', 'EXCEL'; ...
3747 {'.xlsx'}, 'Microsoft Excel transposed (*.xlsx)', 'EXCEL-TR'; ...
3748 };
3749 case 'timefreqout'
3750 argout1 = {...
3751 {'_timefreq'}, 'Brainstorm structure (*timefreq*.mat)', 'BST'; ...
3752 {'.mat'}, 'FieldTrip freq (*.mat)', 'FT-FREQ'; ...
3753 {'.txt'}, 'ASCII: Space-separated, fixed columns size (*.txt)', 'ASCII-SPC'; ...
3754 {'.txt'}, 'ASCII: Space-separated with header, fixed column size (*.txt)', 'ASCII-SPC-HDR'; ...
3755 {'.tsv'}, 'ASCII: Tab-separated (*.tsv)', 'ASCII-TSV'; ...
3756 {'.tsv'}, 'ASCII: Tab-separated with header (*.tsv)', 'ASCII-TSV-HDR'; ...
3757 {'.tsv'}, 'ASCII: Tab-separated with header transposed (*.tsv)', 'ASCII-TSV-HDR-TR'; ...
3758 {'.csv'}, 'ASCII: Comma-separated (*.csv)', 'ASCII-CSV'; ...
3759 {'.csv'}, 'ASCII: Comma-separated with header (*.csv)', 'ASCII-CSV-HDR'; ...
3760 {'.csv'}, 'ASCII: Comma-separated with header transposed (*.csv)', 'ASCII-CSV-HDR-TR'; ...
3761 {'.xlsx'}, 'Microsoft Excel (*.xlsx)', 'EXCEL'; ...
3762 {'.xlsx'}, 'Microsoft Excel transposed (*.xlsx)', 'EXCEL-TR'; ...
3763 };
3764 case 'matrixout'
3765 argout1 = {...
3766 {'_matrix'}, 'Brainstorm structure (*matrix*.mat)', 'BST'; ...
3767 {'.mat'}, 'FieldTrip timelock (*.mat)', 'FT-TIMELOCK'; ...
3768 {'.txt'}, 'ASCII: Space-separated, fixed columns size (*.txt)', 'ASCII-SPC'; ...
3769 {'.txt'}, 'ASCII: Space-separated with header, fixed column size (*.txt)', 'ASCII-SPC-HDR'; ...
3770 {'.tsv'}, 'ASCII: Tab-separated (*.tsv)', 'ASCII-TSV'; ...
3771 {'.tsv'}, 'ASCII: Tab-separated with header (*.tsv)', 'ASCII-TSV-HDR'; ...
3772 {'.tsv'}, 'ASCII: Tab-separated with header transposed (*.tsv)', 'ASCII-TSV-HDR-TR'; ...
3773 {'.csv'}, 'ASCII: Comma-separated (*.csv)', 'ASCII-CSV'; ...
3774 {'.csv'}, 'ASCII: Comma-separated with header (*.csv)', 'ASCII-CSV-HDR'; ...
3775 {'.csv'}, 'ASCII: Comma-separated with header transposed (*.csv)', 'ASCII-CSV-HDR-TR'; ...
3776 {'.xlsx'}, 'Microsoft Excel (*.xlsx)', 'EXCEL'; ...
3777 {'.xlsx'}, 'Microsoft Excel transposed (*.xlsx)', 'EXCEL-TR'; ...
3778 };
3779 case 'montagein'
3780 argout1 = {...
3781 {'.sel'}, 'MNE selection files (*.sel)', 'MNE'; ...
3782 {'.mon'}, 'Text montage files (*.mon)', 'MON'; ...
3783 {'_montage'}, 'Brainstorm montage files (montage_*.mat)', 'BST';
3784 {'.csv'}, 'Comma-separated montage files (*.csv)', 'CSV'; ...
3785 {'.xml'}, 'Compumedics ProFusion montages (*.xml)', 'EEG-COMPUMEDICS-PFS'};
3786 case 'montageout'
3787 argout1 = {...
3788 {'.sel'}, 'MNE selection files (*.sel)', 'MNE'; ...
3789 {'.mon'}, 'Text montage files (*.mon)', 'MON'; ...
3790 {'_montage'}, 'Brainstorm montage files (montage_*.mat)', 'BST'};
3791 case 'fibers'
3792 argout1 = {...
3793 {'.trk'}, 'TrackVis (*.trk)', 'TRK'; ...
3794 {'_fibers'}, 'Brainstorm fibers files (fibers_*.mat)', 'BST'};
3795 end
3796
3797
3798 %% ===== FONTS =====
3799 case 'FigFont'
3800 if ispc
3801 argout1 = 8;
3802 else
3803 argout1 = 9;
3804 end
3805 InterfaceScaling = bst_get('InterfaceScaling');
3806 if (InterfaceScaling ~= 100)
3807 argout1 = argout1 * InterfaceScaling / 100;
3808 end
3809
3810 case 'Font'
3811 % Default font size
3812 if (nargin < 2)
3813 if strncmp(computer,'MAC',3)
3814 fontSize = 12;
3815 else
3816 fontSize = 11;
3817 end
3818 % Font size in input
3819 else
3820 fontSize = varargin{2};
3821 end
3822 % Adjust for interface scaling
3823 fontSize = fontSize * bst_get('InterfaceScaling') / 100;
3824
3825 % Font types
3826 fontTypes = {};
3827 if (nargin >= 3)
3828 fontTypes{end + 1} = varargin{3};
3829 end
3830 fontTypes{end + 1} = 'Arial'; % Default font
3831 fontTypes{end + 1} = 'Liberation Sans'; % Free Arial substitute
3832
3833 % Check for cached font
3834 foundFont = 0;
3835 for iFont = 1 : length(fontTypes)
3836 strCache = strrep(sprintf('%s%d', fontTypes{iFont}, round(fontSize*100)), ' ', '_');
3837 if ~isempty(GlobalData) && isfield(GlobalData, 'Program') && isfield(GlobalData.Program, 'FontCache') && isfield(GlobalData.Program.FontCache, strCache)
3838 argout1 = GlobalData.Program.FontCache.(strCache);
3839 foundFont = 1;
3840 break;
3841 end
3842 end
3843
3844 % If font not cached, find first supported font
3845 if ~foundFont
3846 ge = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment();
3847 allFonts = cell(ge.getAvailableFontFamilyNames());
3848
3849 for iFont = 1 : length(fontTypes)
3850 if any(strcmp(fontTypes{iFont}, allFonts))
3851 fontType = fontTypes{iFont};
3852 foundFont = 1;
3853 break;
3854 end
3855 end
3856
3857 if ~foundFont
3858 fontType = 'SansSerif'; % If nothing else works.
3859 end
3860
3861 strCache = strrep(sprintf('%s%d', fontType, round(fontSize*100)), ' ', '_');
3862 argout1 = java.awt.Font(fontType, java.awt.Font.PLAIN, fontSize);
3863 GlobalData.Program.FontCache.(strCache) = argout1;
3864 end
3865
3866 %% ==== PANEL CONTAINERS ====
3867 case 'PanelContainer'
3868 % Get Brainstorm GUI context structure
3869 bst_GUI = GlobalData.Program.GUI;
3870 if (isempty(bst_GUI) || ~isfield(bst_GUI, 'panelContainers'))
3871 error('Brainstorm GUI is not yet initialized');
3872 end
3873
3874 % Get ContainerName in argument
3875 if ((nargin >= 2) && (ischar(varargin{2})))
3876 ContainerName = varargin{2};
3877 % If no container name in argument : just display all the container names
3878 else
3879 disp('Registered panel containers :');
3880 for iContainer = 1:length(bst_GUI.panelContainers)
3881 disp([' - ' bst_GUI.panelContainers(iContainer).name]);
3882 end
3883 return
3884 end
3885
3886 % Look for containerName in all the registered panel containers
3887 iContainer = 1;
3888 found = 0;
3889 while (~found (iContainer <= length(bst_GUI.panelContainers)))
3890 if (strcmpi(ContainerName, bst_GUI.panelContainers(iContainer).name))
3891 found = 1;
3892 else
3893 iContainer = iContainer + 1;
3894 end
3895 end
3896 % If container is found : return it
3897 if (found)
3898 argout1 = bst_GUI.panelContainers(iContainer).jHandle;
3899 else
3900 % warning('Brainstorm:InvalidContainer', 'Container ''%s'' could not be found.', ContainerName);
3901 end
3902
3903
3904 %% ==== PANELS ====
3905 case 'Panel'
3906 % Get Brainstorm GUI context structure
3907 if (isempty(GlobalData) || isempty(GlobalData.Program.GUI) || ~isfield(GlobalData.Program.GUI, 'panels'))
3908 return
3909 end
3910 listPanels = GlobalData.Program.GUI.panels;
3911 % Get Panel in argument
3912 if ((nargin >= 2) && (ischar(varargin{2})))
3913 PanelName = varargin{2};
3914 % If no panel name in argument : just display all the panels names
3915 else
3916 disp('Registered panels :');
3917 for iContainer = 1:length(listPanels)
3918 disp([' - ' get(listPanels(iContainer), 'name')]);
3919 end
3920 return
3921 end
3922 % Look for panelName in all the registered panels
3923 iPanel = find(strcmpi(PanelName, get(listPanels, 'name')), 1);
3924 if ~isempty(iPanel)
3925 argout1 = listPanels(iPanel);
3926 argout2 = iPanel;
3927 end
3928
3929
3930 %% ==== PANEL CONTROLS ====
3931 % Calls : bst_get('PanelControls', PanelName)
3932 case 'PanelControls'
3933 % Get Panel name in argument
3934 if ((nargin >= 2) && (ischar(varargin{2})))
3935 PanelName = varargin{2};
3936 else
3937 error('Invalid call to bst_get()');
3938 end
3939 % Find BstPanel with this name
3940 bstPanel = bst_get('Panel', PanelName);
3941 % If panel was found : return its controls
3942 if ~isempty(bstPanel)
3943 argout1 = get(bstPanel, 'sControls');
3944 end
3945
3946 %% ===== NODES COPY =====
3947 % Calls : bst_get('Clipboard')
3948 case 'Clipboard'
3949 argout1 = GlobalData.Program.Clipboard.Nodes;
3950 argout2 = GlobalData.Program.Clipboard.isCut;
3951
3952 %% ==== DIRECTORIES ====
3953 case 'DirDefaultSubject'
3954 argout1 = '@default_subject';
3955 case 'DirDefaultStudy'
3956 argout1 = '@default_study';
3957 case 'DirAnalysisIntra'
3958 argout1 = '@intra';
3959 case 'DirAnalysisInter'
3960 argout1 = '@inter';
3961 case 'NormalizedSubjectName'
3962 argout1 = 'Group_analysis';
3963
3964 %% ==== OTHER ====
3965 case 'ResizeFunction'
3966 if (bst_get('MatlabVersion') <= 803)
3967 argout1 = 'ResizeFcn';
3968 else
3969 argout1 = 'SizeChangedFcn';
3970 end
3971 case 'groot'
3972 if (bst_get('MatlabVersion') <= 803)
3973 argout1 = 0;
3974 else
3975 argout1 = groot;
3976 end
3977 case 'JFrame'
3978 hFig = varargin{2};
3979 MatlabVersion = bst_get('MatlabVersion');
3980 jFrame = [];
3981 try
3982 if (MatlabVersion <= 705)
3983 jf = get(hFig, 'javaframe');
3984 jFrame = jf.fFigureClient.getWindow();
3985 elseif (MatlabVersion <= 712)
3986 jf = get(handle(hFig), 'javaframe');
3987 jFrame = jf.fFigureClient.getWindow();
3988 elseif (MatlabVersion <= 803)
3989 jf = get(handle(hFig), 'javaframe');
3990 jFrame = jf.fHG1Client.getWindow();
3991 elseif (MatlabVersion < 907) % Matlab >= 2019b deprecated the JavaFrame property
3992 warning('off', 'MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
3993 jf = get(hFig, 'javaframe');
3994 warning('on', 'MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
3995 jFrame = jf.fHG2Client.getWindow();
3996 else
3997 disp('BST> Error: Matlab 2019b deprecated the JavaFrame property.');
3998 end
3999 catch
4000 disp('BST> Warning: Cannot get the JavaFrame property for the selected figure.');
4001 end
4002 argout1 = jFrame;
4003
4004 %% ==== ERROR ====
4005 otherwise
4006 error(sprintf('Invalid context : "%s"', contextName));
4007 end
4008 end
4009
4010
4011
4012
4013 %% ==== HELPERS ====
4014 % Return all the protocol studies that have a given file in its structures
4015 % Possible field names: Result.DataFile, Result.FileName, Data.FileName, Channel.FileName
4016 %
4017 % USAGE: [sFoundStudy, iFoundStudy, iItem] = findFileInStudies(fieldGroup, fieldName, fieldFile, iStudiesList)
4018 % [sFoundStudy, iFoundStudy, iItem] = findFileInStudies(fieldGroup, fieldName, fieldFile)
4019 function [sFoundStudy, iFoundStudy, iItem] = findFileInStudies(fieldGroup, fieldName, fieldFile, iStudiesList)
4020 global GlobalData;
4021 sFoundStudy = [];
4022 iFoundStudy = [];
4023 iItem = [];
4024 % If no file provided, return
4025 if isempty(fieldFile)
4026 return;
4027 end
4028 % Extract folder(s) of the file(s) we're looking for
4029 fieldParts = strfind(fieldFile, '|');
4030 if ~isempty(fieldParts)
4031 fieldParts(end+1) = length(fieldFile);
4032 fieldFolders = {};
4033 iLast = 1;
4034 for iPart = 1:length(fieldParts)
4035 folder = fileparts(fieldFile(iLast:fieldParts(iPart)-1));
4036 if ~isempty(folder)
4037 fieldFolders{end + 1} = folder;
4038 end
4039 iLast = fieldParts(iPart) + 1;
4040 end
4041 else
4042 fieldFolders = {fileparts(fieldFile)};
4043 end
4044 % Get protocol information
4045 ProtocolStudies = GlobalData.DataBase.ProtocolStudies(GlobalData.DataBase.iProtocol);
4046 % List studies to process
4047 if (nargin < 4) || isempty(iStudiesList)
4048 iStudiesList = [-2, -3, 1:length(ProtocolStudies.Study)];
4049 end
4050
4051 % NORMAL STUDIES: Look for surface file in all the surfaces of all subjects
4052 for iStudy = iStudiesList
4053 % Get study
4054 switch (iStudy)
4055 case -2, sStudy = ProtocolStudies.AnalysisStudy;
4056 case -3, sStudy = ProtocolStudies.DefaultStudy;
4057 otherwise, sStudy = ProtocolStudies.Study(iStudy);
4058 end
4059 % Check if field is available for the study
4060 if isempty(sStudy.(fieldGroup))
4061 continue;
4062 end
4063 % Check we are in the correct folder
4064 if ~any(file_compare(fieldFolders, fileparts(sStudy.FileName)))
4065 continue;
4066 end
4067 % Get list of files from study
4068 filesList = {sStudy.(fieldGroup).(fieldName)};
4069 if isempty(filesList)
4070 continue;
4071 end
4072 % Replace empty cells with empty strings
4073 iValidFiles = find(cellfun(@ischar, filesList));
4074 if isempty(iValidFiles)
4075 continue;
4076 end
4077 % Find target in this list
4078 iItem = find(file_compare(filesList(iValidFiles), fieldFile));
4079 if ~isempty(iItem)
4080 sFoundStudy = sStudy;
4081 iFoundStudy = iStudy;
4082 iItem = iValidFiles(iItem);
4083 return
4084 end
4085 end
4086 end
4087
4088
4089 %% ===== FILL MISSING FIELDS =====
4090 function bstPref = FillMissingFields(PrefName, defPref)
4091 global GlobalData;
4092 if isfield(GlobalData, 'Preferences') && isfield(GlobalData.Preferences, PrefName)
4093 bstPref = GlobalData.Preferences.(PrefName);
4094 bstPref = struct_copy_fields(bstPref, defPref, 0);
4095 else
4096 bstPref = defPref;
4097 end
4098 end
4099
4100
4101
4102
4103
4104
4105
To change parameters or database structures: bst_set.m.
1 function bst_set( varargin )
2 % BST_SET: Set a Brainstorm structure.
3 %
4 % DESCRIPTION: This function is used to abstract the way that these structures are stored.
5 %
6 % USAGE:
7 % ====== DIRECTORIES ==================================================================
8 % - bst_set('BrainstormHomeDir', BrainstormHomeDir)
9 % - bst_set('BrainstormTmpDir', BrainstormTmpDir)
10 % - bst_set('BrainstormDbDir', BrainstormDbDir)
11 % - bst_set('LastUsedDirs', sDirectories)
12 % - bst_set('BrainSuiteDir', BrainSuiteDir)
13 % - bst_set('PythonExe', PythonExe)
14 % - bst_set('PluginCustomPath', PluginCustomPath)
15 %
16 % ====== PROTOCOLS ====================================================================
17 % - bst_set('iProtocol', iProtocol)
18 % - bst_set('ProtocolInfo', sProtocolInfo)
19 % - bst_set('ProtocolSubjects', ProtocolSubjects)
20 % - bst_set('isProtocolLoaded', isProtocolLoaded)
21 % - bst_set('isProtocolModified',isProtocolModified)
22 % - bst_set('ProtocolStudies', ProtocolStudies)
23 % - bst_set('Study', iStudy, sStudy) : Set a study in current protocol
24 % - bst_set('Subject', iSubject, sSubject) : Set a subject in current protocol
25 %
26 % ====== GUI =================================================================
27 % - bst_set('Layout', sLayout)
28 % - bst_set('Layout', PropName, PropValue)
29 % - bst_set('Clipboard', Nodes, isCut) : Copy operation from the tree
30 %
31 % ====== CONFIGURATION =================================================================
32 % - bst_set('Version', Version)
33 % - bst_set('ByteOrder', value) : 'b' for big endian, 'l' for little endian
34 % - bst_set('AutoUpdates', isAutoUpdates)
35 % - bst_set('ExpertMode', isExpertMode)
36 % - bst_set('DisplayGFP', isDisplayGFP)
37 % - bst_set('DownsampleTimeSeries', isDownsampleTimeSeries)
38 % - bst_set('GraphicsSmoothing', isGraphicsSmoothing)
39 % - bst_set('ForceMatCompression', isForceCompression)
40 % - bst_set('IgnoreMemoryWarnings', isIgnoreMemoryWarnings)
41 % - bst_set('SystemCopy', isSystemCopy)
42 % - bst_set('DisableOpenGL', isDisableOpenGL)
43 % - bst_set('InterfaceScaling', InterfaceScaling)
44 % - bst_set('TSDisplayMode', TSDisplayMode) : {'butterfly','column'}
45 % - bst_set('ElectrodeConfig', ElectrodeConfig, Modality)
46 % - bst_set('DefaultFormats' defaultFormats)
47 % - bst_set('BFSProperties', [scalpCond,skullCond,brainCond,scalpThick,skullThick])
48 % - bst_set('ImportEegRawOptions', ImportEegRawOptions)
49 % - bst_set('BugReportOptions', BugReportOptions)
50 % - bst_set('DefaultSurfaceDisplay', displayStruct)
51 % - bst_set('MagneticExtrapOptions', extrapStruct)
52 % - bst_set('TimefreqOptions_morlet', Options)
53 % - bst_set('TimefreqOptions_fft', Options)
54 % - bst_set('TimefreqOptions_psd', Options)
55 % - bst_set('TimefreqOptions_hilbert', Options)
56 % - bst_set('TimefreqOptions_plv', Options)
57 % - bst_set('OpenMEEGOptions', Options)
58 % - bst_set('DuneuroOptions', Options)
59 % - bst_set('GridOptions_headmodel', Options)
60 % - bst_set('GridOptions_dipfit', Options)
61 % - bst_set('UniformizeTimeSeriesScales', isUniform)
62 % - bst_set('FlipYAxis', isFlipY)
63 % - bst_set('AutoScaleY', isAutoScaleY)
64 % - bst_set('FixedScaleY', Modality, Value)
65 % - bst_set('XScale', XScale)
66 % - bst_set('YScale', YScale)
67 % - bst_set('ShowXGrid', isShowXGrid)
68 % - bst_set('ShowYGrid', isShowYGrid)
69 % - bst_set('ShowZeroLines', isShowZeroLines)
70 % - bst_set('ShowEventsMode', ShowEventsMode)
71 % - bst_set('Resolution', [resX,resY])
72 % - bst_set('UseSigProcToolbox', UseSigProcToolbox)
73 % - bst_set('RawViewerOptions', RawViewerOptions)
74 % - bst_set('TopoLayoutOptions', TopoLayoutOptions)
75 % - bst_set('StatThreshOptions', StatThreshOptions)
76 % - bst_set('ContactSheetOptions', ContactSheetOptions)
77 % - bst_set('ProcessOptions', ProcessOptions)
78 % - bst_set('MriOptions', MriOptions)
79 % - bst_set('CustomColormaps', CustomColormaps)
80 % - bst_set('DigitizeOptions', DigitizeOptions)
81 % - bst_set('ReadOnly', ReadOnly)
82 % - bst_set('LastPsdDisplayFunction', LastPsdDisplayFunction)
83 % - bst_set('PlotlyCredentials', Username, ApiKey, Domain)
84 % - bst_set('KlustersExecutable', ExecutablePath)
85 % - bst_set('ExportBidsOptions'), ExportBidsOptions)
86 %
87 % SEE ALSO bst_get
88
89 % @=============================================================================
90 % This function is part of the Brainstorm software:
91 % https://neuroimage.usc.edu/brainstorm
92 %
93 % Copyright (c) University of Southern California & McGill University
94 % This software is distributed under the terms of the GNU General Public License
95 % as published by the Free Software Foundation. Further details on the GPLv3
96 % license can be found at http://www.gnu.org/copyleft/gpl.html.
97 %
98 % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
99 % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
100 % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
101 % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
102 % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
103 %
104 % For more information type "brainstorm license" at command prompt.
105 % =============================================================================@
106 %
107 % Authors: Francois Tadel, 2008-2021
108 % Martin Cousineau, 2017
109
110 global GlobalData;
111
112 %% ==== PARSE INPUTS ====
113 if ((nargin >= 1) && ischar(varargin{1}))
114 contextName = varargin{1};
115 if (nargin >= 2)
116 contextValue = varargin{2};
117 else
118 contextValue = [];
119 end
120 else
121 error('Usage : bst_set(contextName, contextValue)');
122 end
123
124 % Get required context structure
125 switch contextName
126 %% ==== BRAINSTORM CONFIGURATION ====
127 case 'Version'
128 GlobalData.Program.Version = contextValue;
129 case 'BrainstormHomeDir'
130 GlobalData.Program.BrainstormHomeDir = contextValue;
131 case 'BrainstormDbDir'
132 GlobalData.DataBase.BrainstormDbDir = contextValue;
133 case 'BrainstormTmpDir'
134 GlobalData.Preferences.BrainstormTmpDir = contextValue;
135
136 %% ==== PROTOCOL ====
137 case 'iProtocol'
138 if isnumeric(contextValue)
139 GlobalData.DataBase.iProtocol = contextValue;
140 else
141 error('iProtocol should be a number.');
142 end
143 case {'ProtocolSubjects', 'ProtocolStudies'}
144 for structField = fieldnames(contextValue)'
145 GlobalData.DataBase.(contextName)(GlobalData.DataBase.iProtocol).(structField{1}) = contextValue.(structField{1});
146 end
147 GlobalData.DataBase.isProtocolModified(GlobalData.DataBase.iProtocol) = 1;
148 case 'ProtocolInfo'
149 for structField = fieldnames(contextValue)'
150 GlobalData.DataBase.(contextName)(GlobalData.DataBase.iProtocol).(structField{1}) = contextValue.(structField{1});
151 end
152 case 'isProtocolLoaded'
153 GlobalData.DataBase.isProtocolLoaded(GlobalData.DataBase.iProtocol) = contextValue;
154 case 'isProtocolModified'
155 GlobalData.DataBase.isProtocolModified(GlobalData.DataBase.iProtocol) = contextValue;
156
157 %% ==== SUBJECT ====
158 case 'Subject'
159 % Get subjects list
160 ProtocolSubjects = bst_get('ProtocolSubjects');
161 iSubject = varargin{2};
162 sSubject = varargin{3};
163 % If default subject
164 if (iSubject == 0)
165 ProtocolSubjects.DefaultSubject = sSubject;
166 else
167 ProtocolSubjects.Subject(iSubject) = sSubject;
168 end
169 % Update DataBase
170 bst_set('ProtocolSubjects', ProtocolSubjects);
171
172
173 %% ==== STUDY ====
174 case 'Study'
175 % Get studies list
176 ProtocolStudies = bst_get('ProtocolStudies');
177 iStudies = varargin{2};
178 sStudies = varargin{3};
179 iAnalysisStudy = -2;
180 iDefaultStudy = -3;
181 for i = 1:length(iStudies)
182 % Normal study
183 if (iStudies(i) > 0)
184 ProtocolStudies.Study(iStudies(i)) = sStudies(i);
185 % Inter-subject analysis study
186 elseif (iStudies(i) == iAnalysisStudy)
187 ProtocolStudies.AnalysisStudy = sStudies(i);
188 % Default study
189 elseif (iStudies(i) == iDefaultStudy)
190 ProtocolStudies.DefaultStudy = sStudies(i);
191 end
192 end
193 % Update DataBase
194 bst_set('ProtocolStudies', ProtocolStudies);
195
196
197 %% ==== GUI ====
198 % USAGE: bst_set('Layout', sLayout)
199 % bst_set('Layout', PropName, PropValue)
200 case 'Layout'
201 if (nargin == 2) && isstruct(contextValue)
202 GlobalData.Preferences.Layout = contextValue;
203 isUpdateScreens = 0;
204 elseif (nargin == 3) && ischar(contextValue) && isfield(GlobalData.Preferences, 'Layout') && isfield(GlobalData.Preferences.Layout, contextValue)
205 GlobalData.Preferences.Layout.(contextValue) = varargin{3};
206 isUpdateScreens = strcmpi(contextValue, 'DoubleScreen');
207 else
208 error('Invalid call to bst_set.');
209 end
210 % Update screen configuration
211 GlobalData.Program.ScreenDef = gui_layout('GetScreenClientArea');
212 % Update layout right now
213 gui_layout('Update');
214 % If the number of screen was changed: update the maximum size of the Brainstorm window
215 if isUpdateScreens
216 gui_layout('UpdateMaxBstSize');
217 end
218
219 % USAGE: bst_set('FixedScaleY', [])
220 % bst_set('FixedScaleY', Modality, Value)
221 case 'FixedScaleY'
222 if (nargin == 3) && ~isempty(contextValue) && ~isempty(varargin{3})
223 GlobalData.Preferences.FixedScaleY.(contextValue) = varargin{3};
224 elseif (nargin == 2) && isempty(contextValue)
225 GlobalData.Preferences.FixedScaleY = struct();
226 end
227
228 case 'ByteOrder'
229 switch(contextValue)
230 case {'b','ieee-le','n'}
231 GlobalData.Preferences.ByteOrder = 'b';
232 case {'l','ieee-be'}
233 GlobalData.Preferences.ByteOrder = 'l';
234 otherwise
235 error('Invalid byte order.');
236 end
237
238 case 'Clipboard'
239 if (length(varargin) >= 3)
240 isCut = varargin{3};
241 else
242 isCut = 0;
243 end
244 GlobalData.Program.Clipboard.Nodes = contextValue;
245 GlobalData.Program.Clipboard.isCut = isCut;
246
247 case 'ElectrodeConfig'
248 Modality = varargin{2};
249 ElectrodeConf = varargin{3};
250 if ~ismember(Modality, {'EEG','SEEG','ECOG'})
251 error(['Invalid modality: ' Modality]);
252 end
253 GlobalData.Preferences.(contextName).(Modality) = ElectrodeConf;
254
255 case {'UniformizeTimeSeriesScales', 'XScale', 'YScale', 'FlipYAxis', 'AutoScaleY', 'ShowXGrid', 'ShowYGrid', 'ShowZeroLines', 'ShowEventsMode', ...
256 'Resolution', 'AutoUpdates', 'ExpertMode', 'DisplayGFP', 'ForceMatCompression', 'GraphicsSmoothing', 'DownsampleTimeSeries', ...
257 'DisableOpenGL', 'InterfaceScaling', 'TSDisplayMode', 'UseSigProcToolbox', 'LastUsedDirs', 'DefaultFormats', ...
258 'BFSProperties', 'ImportDataOptions', 'ImportEegRawOptions', 'RawViewerOptions', 'MontageOptions', 'TopoLayoutOptions', ...
259 'StatThreshOptions', 'ContactSheetOptions', 'ProcessOptions', 'BugReportOptions', 'DefaultSurfaceDisplay', ...
260 'MagneticExtrapOptions', 'MriOptions', 'ConnectGraphOptions', 'NodelistOptions', 'IgnoreMemoryWarnings', 'SystemCopy', ...
261 'TimefreqOptions_morlet', 'TimefreqOptions_hilbert', 'TimefreqOptions_fft', 'TimefreqOptions_psd', 'TimefreqOptions_plv', ...
262 'OpenMEEGOptions', 'DuneuroOptions', 'DigitizeOptions', 'CustomColormaps', 'PluginCustomPath', 'BrainSuiteDir', 'PythonExe', ...
263 'GridOptions_headmodel', 'GridOptions_dipfit', 'LastPsdDisplayFunction', 'KlustersExecutable', 'ExportBidsOptions'}
264 GlobalData.Preferences.(contextName) = contextValue;
265
266 case 'ReadOnly'
267 GlobalData.DataBase.isReadOnly = contextValue;
268
269 case 'PlotlyCredentials'
270 if length(varargin) ~= 4
271 error('Invalid call to bst_set.');
272 end
273 [username, apiKey, domain] = varargin{2:4};
274
275 if isempty(domain)
276 % Default Plot.ly server
277 domain = 'http://plot.ly';
278 end
279
280 % Plotly needs a URL with HTTP and no trailing slash.
281 if strfind(domain, 'https://')
282 domain = strrep(domain, 'https://', 'http://');
283 elseif isempty(strfind(domain, 'http://'))
284 domain = ['http://', domain];
285 end
286 if domain(end) == '/'
287 domain = domain(1:end-1);
288 end
289
290 saveplotlycredentials(username, apiKey);
291 saveplotlyconfig(domain);
292
293 %% ==== ERROR ====
294 otherwise
295 error('Invalid context : ''%s''', contextName);
296
297
298 end
299
300
301
302
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_headmodel: Copy a head model to other folders
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
notesFor 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 =
3In 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 7The 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).
Find 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 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
1 function tutorial_introduction(tutorial_dir, reports_dir)
2 % TUTORIAL_INTRODUCTION: Script that runs all the Brainstorm introduction tutorials.
3 %
4 % INPUTS:
5 % - tutorial_dir : Directory where the sample_introduction.zip file has been unzipped
6 % - reports_dir : Directory where to save the execution report (instead of displaying it)
7
8 % @=============================================================================
9 % This function is part of the Brainstorm software:
10 % https://neuroimage.usc.edu/brainstorm
11 %
12 % Copyright (c) University of Southern California & McGill University
13 % This software is distributed under the terms of the GNU General Public License
14 % as published by the Free Software Foundation. Further details on the GPLv3
15 % license can be found at http://www.gnu.org/copyleft/gpl.html.
16 %
17 % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
18 % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
19 % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
20 % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
21 % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
22 %
23 % For more information type "brainstorm license" at command prompt.
24 % =============================================================================@
25 %
26 % Author: Francois Tadel, 2016-2017
27
28
29 % ===== FILES TO IMPORT =====
30 % Output folder for reports
31 if (nargin < 2) || isempty(reports_dir) || ~isdir(reports_dir)
32 reports_dir = [];
33 end
34 % You have to specify the folder in which the tutorial dataset is unzipped
35 if (nargin == 0) || isempty(tutorial_dir) || ~file_exist(tutorial_dir)
36 error('The first argument must be the full path to the dataset folder.');
37 end
38 % Subject name
39 SubjectName = 'Subject01';
40 % Build the path of the files to import
41 AnatDir = fullfile(tutorial_dir, 'sample_introduction', 'anatomy');
42 Run1File = fullfile(tutorial_dir, 'sample_introduction', 'data', 'S01_AEF_20131218_01_600Hz.ds');
43 Run2File = fullfile(tutorial_dir, 'sample_introduction', 'data', 'S01_AEF_20131218_02_600Hz.ds');
44 NoiseFile = fullfile(tutorial_dir, 'sample_introduction', 'data', 'S01_Noise_20131218_02_600Hz.ds');
45 % Check if the folder contains the required files
46 if ~file_exist(Run1File)
47 error(['The folder ' tutorial_dir ' does not contain the folder from the file sample_introduction.zip.']);
48 end
49 % Re-inialize random number generator
50 if (bst_get('MatlabVersion') >= 712)
51 rng('default');
52 end
53
54
55 %% ===== TUTORIAL #1: CREATE PROTOCOL ================================================
56 % ===================================================================================
57 disp([10 'DEMO> Tutorial #1: Create protocol' 10]);
58 % The protocol name has to be a valid folder name (no spaces, no weird characters...)
59 ProtocolName = 'TutorialIntroduction';
60 % Start brainstorm without the GUI
61 if ~brainstorm('status')
62 brainstorm nogui
63 end
64 % Delete existing protocol
65 gui_brainstorm('DeleteProtocol', ProtocolName);
66 % Create new protocol
67 gui_brainstorm('CreateProtocol', ProtocolName, 0, 0);
68 % Start a new report
69 bst_report('Start');
70 % Reset colormaps
71 bst_colormaps('RestoreDefaults', 'meg');
72 % Set the current display mode to 'butterfly'
73 bst_set('TSDisplayMode', 'butterfly');
74
75
76 %% ===== TUTORIAL #2: IMPORT ANATOMY =================================================
77 % ===================================================================================
78 disp([10 'DEMO> Tutorial #2: Import anatomy' 10]);
79 % Process: Import FreeSurfer folder
80 bst_process('CallProcess', 'process_import_anatomy', [], [], ...
81 'subjectname', SubjectName, ...
82 'mrifile', {AnatDir, 'FreeSurfer'}, ...
83 'nvertices', 15000, ...
84 'nas', [127, 213, 139], ...
85 'lpa', [ 52, 113, 96], ...
86 'rpa', [202, 113, 91]);
87 % This automatically calls the SPM registration procedure because the AC/PC/IH points are not defined
88
89
90
91 %% ===== TUTORIAL #3: EXPLORE ANATOMY ================================================
92 % ===================================================================================
93 disp([10 'DEMO> Tutorial #3: Explore anatomy' 10]);
94 % Get subject definition
95 sSubject = bst_get('Subject', SubjectName);
96 % Get MRI file and surface files
97 MriFile = sSubject.Anatomy(sSubject.iAnatomy).FileName;
98 CortexFile = sSubject.Surface(sSubject.iCortex).FileName;
99 HeadFile = sSubject.Surface(sSubject.iScalp).FileName;
100 % Display MRI
101 hFigMri1 = view_mri(MriFile);
102 hFigMri3 = view_mri_3d(MriFile, [], [], 'NewFigure');
103 hFigMri2 = view_mri_slices(MriFile, 'x', 20);
104 pause(0.5);
105 % Close figures
106 close([hFigMri1 hFigMri2 hFigMri3]);
107 % Display scalp and cortex
108 hFigSurf = view_surface(HeadFile);
109 hFigSurf = view_surface(CortexFile, [], [], hFigSurf);
110 hFigMriSurf = view_mri(MriFile, CortexFile);
111 % Figure configuration
112 iTess = 2;
113 panel_surface('SetShowSulci', hFigSurf, iTess, 1);
114 panel_surface('SetSurfaceColor', hFigSurf, iTess, [1 0 0]);
115 panel_surface('SetSurfaceSmooth', hFigSurf, iTess, 0.5, 0);
116 panel_surface('SetSurfaceTransparency', hFigSurf, iTess, 0.8);
117 figure_3d('SetStandardView', hFigSurf, 'left');
118 pause(0.5);
119 % Close figures
120 close([hFigSurf hFigMriSurf]);
121
122
123
124 %% ===== TUTORIAL #4: CHANNEL FILE ===================================================
125 % ===================================================================================
126 disp([10 'DEMO> Tutorial #4: Channel file' 10]);
127 % Process: Create link to raw files
128 sFilesRun1 = bst_process('CallProcess', 'process_import_data_raw', [], [], ...
129 'subjectname', SubjectName, ...
130 'datafile', {Run1File, 'CTF'}, ...
131 'channelalign', 1);
132 sFilesRun2 = bst_process('CallProcess', 'process_import_data_raw', [], [], ...
133 'subjectname', SubjectName, ...
134 'datafile', {Run2File, 'CTF'}, ...
135 'channelalign', 1);
136 sFilesNoise = bst_process('CallProcess', 'process_import_data_raw', [], [], ...
137 'subjectname', SubjectName, ...
138 'datafile', {NoiseFile, 'CTF'}, ...
139 'channelalign', 0);
140 sFilesRaw = [sFilesRun1, sFilesRun2, sFilesNoise];
141 % Process: Snapshot: Sensors/MRI registration
142 bst_process('CallProcess', 'process_snapshot', [sFilesRun1, sFilesRun2], [], ...
143 'target', 1, ... % Sensors/MRI registration
144 'modality', 1, ... % MEG (All)
145 'orient', 1, ... % left
146 'Comment', 'MEG/MRI Registration');
147
148 % View sensors
149 hFig = view_surface(HeadFile);
150 hFig = view_channels(sFilesRun1.ChannelFile, 'MEG', 1, 1, hFig);
151 % Hide sensors
152 pause(0.5);
153 hFig = view_channels(sFilesRun1.ChannelFile, 'MEG', 0, 0, hFig);
154 % View coils
155 hFig = view_channels(sFilesRun1.ChannelFile, 'CTF', 1, 1, hFig);
156 % View helmet
157 pause(0.5);
158 hFig = view_helmet(sFilesRun1.ChannelFile, hFig);
159 pause(0.5);
160 close(hFig);
161 % Edit good/bad channel for current file
162 gui_edit_channel(sFilesRun1.ChannelFile);
163 pause(0.5);
164 % Unload everything
165 bst_memory('UnloadAll', 'Forced');
166
167
168
169 %% ===== TUTORIAL #5: REVIEW RAW =====================================================
170 % ===================================================================================
171 disp([10 'DEMO> Tutorial #5: Review raw' 10]);
172 % Process: Convert to continuous (CTF): Continuous
173 bst_process('CallProcess', 'process_ctf_convert', sFilesRaw, [], ...
174 'rectype', 2); % Continuous
175
176 % View recordings
177 hFigMeg = view_timeseries(sFilesRun1.FileName, 'MEG');
178 hFigEeg = view_timeseries(sFilesRun1.FileName, 'Misc');
179 hFigSel = view_timeseries(sFilesRun1.FileName, 'MEG', {'MLT11','MLT12','MLT13'});
180 % Figure configuration
181 pause(0.5);
182 panel_record('SetTimeLength', 3);
183 panel_record('SetStartTime', 100);
184 panel_record('SetDisplayMode', hFigMeg, 'column');
185 panel_montage('SetCurrentMontage', hFigMeg, 'CTF LT');
186 % Set filters: panel_filter('SetFilters', LowPassEnabled, LowPassValue, HighPassEnabled, HighPassValue, SinRemovalEnabled, SinRemovalValue, MirrorEnabled, FullSourcesEnabled)
187 panel_filter('SetFilters', 1, 100, 1, 1, 0, [], 0, 0);
188 pause(0.5);
189 panel_record('SetDisplayMode', hFigMeg, 'butterfly');
190 panel_montage('SetCurrentMontage', hFigMeg, '');
191 % Close figures
192 close([hFigMeg hFigEeg hFigSel]);
193
194
195
196 %% ===== TUTORIAL #8: STIM DELAYS ====================================================
197 % ===================================================================================
198 disp([10 'DEMO> Tutorial #8: Stim delays' 10]);
199 % Process: Detect: standard_fix
200 bst_process('CallProcess', 'process_evt_detect_analog', [sFilesRun1, sFilesRun2], [], ...
201 'eventname', 'standard_fix', ...
202 'channelname', 'UADC001', ...
203 'timewindow', [], ...
204 'threshold', 1.2, ...
205 'blanking', 0.2, ...
206 'highpass', 0, ...
207 'lowpass', 0, ...
208 'refevent', 'standard', ...
209 'isfalling', 0, ...
210 'ispullup', 0, ...
211 'isclassify', 0);
212 % Process: Detect: deviant_fix
213 bst_process('CallProcess', 'process_evt_detect_analog', [sFilesRun1, sFilesRun2], [], ...
214 'eventname', 'deviant_fix', ...
215 'channelname', 'UADC001', ...
216 'timewindow', [], ...
217 'threshold', 1.2, ...
218 'blanking', 0.2, ...
219 'highpass', 0, ...
220 'lowpass', 0, ...
221 'refevent', 'deviant', ...
222 'isfalling', 0, ...
223 'ispullup', 0, ...
224 'isclassify', 0);
225 % Process: Read from channel
226 bst_process('CallProcess', 'process_evt_read', [sFilesRun1, sFilesRun2], [], ...
227 'stimchan', 'UDIO001', ...
228 'trackmode', 1, ... % Value: detect the changes of channel value
229 'zero', 0);
230
231 % Process: Delete events
232 bst_process('CallProcess', 'process_evt_delete', [sFilesRun1, sFilesRun2], [], ...
233 'eventname', 'standard, deviant, button');
234 % Process: Rename event (standard_fix>standard)
235 bst_process('CallProcess', 'process_evt_rename', [sFilesRun1, sFilesRun2], [], ...
236 'src', 'standard_fix', ...
237 'dest', 'standard');
238 % Process: Rename event (deviant_fix>deviant)
239 bst_process('CallProcess', 'process_evt_rename', [sFilesRun1, sFilesRun2], [], ...
240 'src', 'deviant_fix', ...
241 'dest', 'deviant');
242 % Process: Rename event (64>button)
243 bst_process('CallProcess', 'process_evt_rename', [sFilesRun1, sFilesRun2], [], ...
244 'src', '64', ...
245 'dest', 'button');
246
247
248
249 %% ===== TUTORIAL #10: FREQUENCY FILTERS =============================================
250 % ===================================================================================
251 disp([10 'DEMO> Tutorial #10: Frequency filters' 10]);
252 % Process: Sinusoid removal: 60Hz 120Hz 180Hz 300Hz
253 sFilesNotch = bst_process('CallProcess', 'process_notch', sFilesRaw, [], ...
254 'freqlist', [60, 120, 180], ...
255 'sensortypes', 'MEG', ...
256 'read_all', 0);
257 % Process: Power spectrum density (Welch)
258 sFilesPsd = bst_process('CallProcess', 'process_psd', [sFilesRaw, sFilesNotch], [], ...
259 'timewindow', [], ...
260 'win_length', 4, ...
261 'win_overlap', 50, ...
262 'clusters', {}, ...
263 'sensortypes', 'MEG', ...
264 'edit', struct(...
265 'Comment', 'Power', ...
266 'TimeBands', [], ...
267 'Freqs', [], ...
268 'ClusterFuncTime', 'none', ...
269 'Measure', 'power', ...
270 'Output', 'all', ...
271 'SaveKernel', 0));
272 % Process: Snapshot: Frequency spectrum
273 bst_process('CallProcess', 'process_snapshot', sFilesPsd, [], ...
274 'target', 10, ... % Frequency spectrum
275 'modality', 1, ... % MEG (All)
276 'Comment', 'Power spectrum density');
277 % Process: Delete folders
278 bst_process('CallProcess', 'process_delete', sFilesRaw, [], ...
279 'target', 2); % Delete folders
280 % Separate the three outputs
281 sFilesRun1 = {sFilesNotch(1).FileName};
282 sFilesRun2 = {sFilesNotch(2).FileName};
283 sFilesNoise = {sFilesNotch(3).FileName};
284
285
286
287 %% ===== TUTORIAL #11: BAD CHANNELS ==================================================
288 % ===================================================================================
289 % % Process: Set bad channels
290 % sFiles = bst_process('CallProcess', 'process_channel_setbad', sFilesRun2, [], ...
291 % 'sensortypes', 'MRT51, MLO52, MLO42, MLO43');
292
293
294
295 %% ===== TUTORIAL #12: ARTIFACTS DETECTION ===========================================
296 % ===================================================================================
297 disp([10 'DEMO> Tutorial #12: Artifacts detection' 10]);
298 % Process: Detect heartbeats
299 bst_process('CallProcess', 'process_evt_detect_ecg', [sFilesRun1, sFilesRun2], [], ...
300 'channelname', 'ECG', ...
301 'timewindow', [], ...
302 'eventname', 'cardiac');
303 % Process: Detect eye blinks
304 bst_process('CallProcess', 'process_evt_detect_eog', [sFilesRun1, sFilesRun2], [], ...
305 'channelname', 'VEOG', ...
306 'timewindow', [], ...
307 'eventname', 'blink');
308 % Process: Remove simultaneous
309 bst_process('CallProcess', 'process_evt_remove_simult', [sFilesRun1, sFilesRun2], [], ...
310 'remove', 'cardiac', ...
311 'target', 'blink', ...
312 'dt', 0.25, ...
313 'rename', 0);
314
315
316
317 %% ===== TUTORIAL #13: SSP ===========================================================
318 % ===================================================================================
319 disp([10 'DEMO> Tutorial #13: SSP' 10]);
320 % Process: SSP ECG: cardiac
321 bst_process('CallProcess', 'process_ssp_ecg', [sFilesRun1, sFilesRun2], [], ...
322 'eventname', 'cardiac', ...
323 'sensortypes', 'MEG', ...
324 'usessp', 0, ...
325 'select', 1);
326 % Process: SSP EOG: blink
327 bst_process('CallProcess', 'process_ssp_eog', sFilesRun1, [], ...
328 'eventname', 'blink', ...
329 'sensortypes', 'MEG', ...
330 'usessp', 0, ...
331 'select', [1 2]);
332 bst_process('CallProcess', 'process_ssp_eog', sFilesRun2, [], ...
333 'eventname', 'blink', ...
334 'sensortypes', 'MEG', ...
335 'usessp', 0, ...
336 'select', 1);
337
338
339 %% ===== TUTORIAL #14: BAD SEGMENTS ==================================================
340 % ===================================================================================
341 disp([10 'DEMO> Tutorial #14: Bad segments' 10]);
342 % Process: Detect other artifacts
343 bst_process('CallProcess', 'process_evt_detect_badsegment', [sFilesRun1, sFilesRun2], [], ...
344 'timewindow', [], ...
345 'sensortypes', 'MEG', ...
346 'threshold', 3, ... % 3
347 'isLowFreq', 1, ...
348 'isHighFreq', 1);
349
350 % Process: Rename event (1-7Hz > saccade) (Run02 only)
351 bst_process('CallProcess', 'process_evt_rename', sFilesRun2, [], ...
352 'src', '1-7Hz', ...
353 'dest', 'saccade');
354
355 % Manual selection of saccades (cannot be done from the pipeline editor: manual edition of the structures)
356 sMatRun2 = in_bst_data(sFilesRun2{1}, 'F');
357 iEvtSaccade = find(strcmpi({sMatRun2.F.events.label}, 'saccade'));
358 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];
359 sMatRun2.F.events(iEvtSaccade).epochs = ones(1, size(sMatRun2.F.events(iEvtSaccade).times, 2));
360 sMatRun2.F.events(iEvtSaccade).channels = cell(1, size(sMatRun2.F.events(iEvtSaccade).times, 2));
361 sMatRun2.F.events(iEvtSaccade).notes = cell(1, size(sMatRun2.F.events(iEvtSaccade).times, 2));
362 bst_save(file_fullpath(sFilesRun2{1}), sMatRun2, 'v6', 1);
363
364 % Process: SSP: saccade (Run02 only)
365 bst_process('CallProcess', 'process_ssp', sFilesRun2, [], ...
366 'timewindow', [], ...
367 'eventname', 'saccade', ...
368 'eventtime', [-0.2, 0.2], ...
369 'bandpass', [1.5, 7], ...
370 'sensortypes', 'MEG', ...
371 'usessp', 1, ...
372 'saveerp', 0, ...
373 'method', 1, ...
374 'select', 1);
375 % Process: Detect other artifacts (Run02 only)
376 bst_process('CallProcess', 'process_evt_detect_badsegment', sFilesRun2, [], ...
377 'timewindow', [], ...
378 'sensortypes', 'MEG', ...
379 'threshold', 3, ... % 3
380 'isLowFreq', 1, ...
381 'isHighFreq', 1);
382
383 % Process: Rename event (1-7Hz > bad_1-7Hz)
384 bst_process('CallProcess', 'process_evt_rename', [sFilesRun1, sFilesRun2], [], ...
385 'src', '1-7Hz', ...
386 'dest', 'bad_1-7Hz');
387 % Process: Rename event (40-240Hz > bad_40-240Hz)
388 bst_process('CallProcess', 'process_evt_rename', [sFilesRun1, sFilesRun2], [], ...
389 'src', '40-240Hz', ...
390 'dest', 'bad_40-240Hz');
391 % Process: Snapshot: SSP projectors
392 bst_process('CallProcess', 'process_snapshot', [sFilesRun1, sFilesRun2], [], ...
393 'target', 2, ... % SSP projectors
394 'Comment', 'SSP projectors');
395
396
397
398 %% ===== TUTORIAL #15: IMPORT EVENTS =================================================
399 % ===================================================================================
400 disp([10 'DEMO> Tutorial #15: Import events' 10]);
401 % Process: Import MEG/EEG: Events (Run01)
402 sFilesEpochs1 = bst_process('CallProcess', 'process_import_data_event', sFilesRun1, [], ...
403 'subjectname', SubjectName, ...
404 'condition', '', ...
405 'eventname', 'standard, deviant', ...
406 'timewindow', [], ...
407 'epochtime', [-0.100, 0.500], ...
408 'createcond', 0, ...
409 'ignoreshort', 1, ...
410 'usectfcomp', 1, ...
411 'usessp', 1, ...
412 'freq', [], ...
413 'baseline', [-0.1, -0.0017]);
414 % Process: Import MEG/EEG: Events (Run02)
415 sFilesEpochs2 = bst_process('CallProcess', 'process_import_data_event', sFilesRun2, [], ...
416 'subjectname', SubjectName, ...
417 'condition', '', ...
418 'eventname', 'standard, deviant', ...
419 'timewindow', [], ...
420 'epochtime', [-0.100, 0.500], ...
421 'createcond', 0, ...
422 'ignoreshort', 1, ...
423 'usectfcomp', 1, ...
424 'usessp', 1, ...
425 'freq', [], ...
426 'baseline', [-0.1, -0.0017]);
427 % Display raster plot
428 hFigRaster = view_erpimage({sFilesEpochs1.FileName}, 'erpimage', 'MEG');
429 panel_display();
430 bst_report('Snapshot', hFigRaster, sFilesEpochs1(1).FileName, 'ERP image');
431 close(hFigRaster);
432
433
434 %% ===== TUTORIAL #16: AVERAGE =======================================================
435 % ===================================================================================
436 disp([10 'DEMO> Tutorial #16: Average' 10]);
437 % Process: Average: By trial group (folder average)
438 sFilesAvg = bst_process('CallProcess', 'process_average', [sFilesEpochs1, sFilesEpochs2], [], ...
439 'avgtype', 5, ... % By trial groups (folder average)
440 'avg_func', 1, ... % Arithmetic average: mean(x)
441 'weighted', 0, ...
442 'keepevents', 1);
443 % Process: Delete events 'cardiac'
444 bst_process('CallProcess', 'process_evt_delete', sFilesAvg, [], ...
445 'eventname', 'cardiac');
446 % Process: Snapshot: Recordings time series
447 bst_process('CallProcess', 'process_snapshot', sFilesAvg, [], ...
448 'target', 5, ... % Recordings time series
449 'modality', 1, ... % MEG (All)
450 'Comment', 'Evoked response');
451 % Set colormap: global color scale
452 bst_colormaps('SetMaxMode', 'meg', 'global');
453 % Process: Snapshot: Recordings topography (contact sheet)
454 bst_process('CallProcess', 'process_snapshot', sFilesAvg, [], ...
455 'target', 7, ... % Recordings topography (contact sheet)
456 'modality', 1, ... % MEG
457 'contact_time', [0, 0.350], ...
458 'contact_nimage', 15, ...
459 'Comment', 'Evoked response');
460
461 % Process: Average+Stderr: By trial group (subject average)
462 sFilesAvgAll = bst_process('CallProcess', 'process_average', [sFilesEpochs1, sFilesEpochs2], [], ...
463 'avgtype', 6, ... % By trial group (subject average)
464 'avg_func', 7, ... % Arithmetic average + Standard error
465 'weighted', 0, ...
466 'keepevents', 1);
467 % Process: Delete events 'cardiac'
468 bst_process('CallProcess', 'process_evt_delete', sFilesAvgAll, [], ...
469 'eventname', 'cardiac');
470 % Process: Delete events 'saccade'
471 bst_process('CallProcess', 'process_evt_delete', sFilesAvgAll, [], ...
472 'eventname', 'saccade');
473 % Process: Snapshot: Recordings time series
474 bst_process('CallProcess', 'process_snapshot', sFilesAvgAll, [], ...
475 'target', 5, ... % Recordings time series
476 'modality', 1, ... % MEG (All)
477 'Comment', 'Evoked response');
478
479
480 %% ===== TUTORIAL #17: EXPLORATION ===================================================
481 % ===================================================================================
482 disp([10 'DEMO> Tutorial #17: Bad segments' 10]);
483 % View averages
484 hFigMeg1 = view_timeseries(sFilesAvg(1).FileName, 'MEG');
485 hFigMeg2 = view_timeseries(sFilesAvg(2).FileName, 'MEG');
486 hFigEeg1 = view_timeseries(sFilesAvg(1).FileName, 'Misc');
487 hFigEeg2 = view_timeseries(sFilesAvg(2).FileName, 'Misc');
488 hFigTopo1 = view_topography(sFilesAvg(1).FileName, 'MEG', '2DSensorCap');
489 hFigTopo2 = view_topography(sFilesAvg(2).FileName, 'MEG', '2DSensorCap');
490 hFigTp2 = view_topography(sFilesAvg(3).FileName, 'MEG', '3DSensorCap');
491 hFigTp3 = view_topography(sFilesAvg(3).FileName, 'MEG', '2DDisc');
492 hFigTp4 = view_topography(sFilesAvg(3).FileName, 'MEG', '2DLayout');
493 % Set time: 90ms
494 panel_time('SetCurrentTime', 0.090);
495 % Set filters: 40Hz low-pass, no high-pass
496 panel_filter('SetFilters', 1, 40, 0, [], 0, [], 0, 0);
497 % View selected sensors
498 SelectedChannels = {'MLC31', 'MLC32'};
499 bst_figures('SetSelectedRows', SelectedChannels);
500 view_timeseries(sFilesAvg(4).FileName, [], SelectedChannels);
501 % Select time window
502 figure_timeseries('SetTimeSelectionManual', hFigMeg1, [0.070, 0.130]);
503 % Show sensors on 2DSensorCap topography
504 isMarkers = 1;
505 isLabels = 0;
506 figure_3d('ViewSensors', hFigTopo1, isMarkers, isLabels);
507 % Display time contact sheet for a figure
508 pause(0.5);
509 hContactFig = view_contactsheet( hFigTopo2, 'time', 'fig', [], 12, [0 0.120] );
510 pause(0.5);
511 close(hContactFig);
512
513
514
515 %% ===== TUTORIAL #18: COLORMAPS =====================================================
516 % ===================================================================================
517 disp([10 'DEMO> Tutorial #18: Colormaps' 10]);
518 % Set 'Meg' colormap to 'jet'
519 bst_colormaps('SetColormapName', 'meg', 'jet');
520 pause(0.5);
521 % Set 'Meg' colormap to 'rwb'
522 bst_colormaps('SetColormapName', 'meg', 'cmap_rbw');
523 % Set colormap to display absolute values
524 bst_colormaps('SetColormapAbsolute', 'meg', 1);
525 % Normalize colormap for each time frame
526 bst_colormaps('SetMaxMode', 'meg', 'local');
527 % Hide colorbar
528 bst_colormaps('SetDisplayColorbar', 'meg', 0);
529 pause(0.5);
530 % Restore colormap to default values
531 bst_colormaps('RestoreDefaults', 'meg');
532 % Edit good/bad channel for current file
533 gui_edit_channelflag(sFilesAvg(1).FileName);
534 % Close figures
535 pause(0.5);
536 bst_memory('UnloadAll', 'Forced');
537
538
539
540 %% ===== TUTORIAL #20: HEAD MODEL ====================================================
541 % ===================================================================================
542 disp([10 'DEMO> Tutorial #20: Head model' 10]);
543 % Process: Compute head model
544 bst_process('CallProcess', 'process_headmodel', sFilesAvg, [], ...
545 'comment', '', ...
546 'sourcespace', 1, ...
547 'meg', 3); % Overlapping spheres
548 % Get study structure
549 sStudy = bst_get('Study', sFilesAvg(1).iStudy);
550 % Show spheres
551 hFig = view_spheres(sStudy.HeadModel(sStudy.iHeadModel).FileName, sStudy.Channel.FileName, sSubject);
552 pause(0.5);
553 close(hFig);
554
555
556
557 %% ===== TUTORIAL #21: NOISE COVARIANCE ==============================================
558 % ===================================================================================
559 disp([10 'DEMO> Tutorial #21: Noise covariance' 10]);
560 % Process: Compute covariance (noise or data)
561 bst_process('CallProcess', 'process_noisecov', sFilesNoise, [], ...
562 'baseline', [], ...
563 'sensortypes', 'MEG, EEG, SEEG, ECOG', ...
564 'target', 1, ... % Noise covariance (covariance over baseline time window)
565 'dcoffset', 1, ... % Block by block, to avoid effects of slow shifts in data
566 'identity', 0, ...
567 'copycond', 1, ...
568 'copysubj', 0, ...
569 'replacefile', 1); % Replace
570 % Process: Snapshot: Noise covariance
571 bst_process('CallProcess', 'process_snapshot', sFilesNoise, [], ...
572 'target', 3, ... % Noise covariance
573 'Comment', 'Noise covariance');
574
575 % Process: Compute covariance (noise or data) [Run01]
576 bst_process('CallProcess', 'process_noisecov', sFilesEpochs1, [], ...
577 'baseline', [-0.1, -0.0017], ...
578 'datatimewindow', [0, 0.5], ...
579 'sensortypes', 'MEG, EEG, SEEG, ECOG', ...
580 'target', 2, ... % Data covariance (covariance over data time window)
581 'dcoffset', 1, ... % Block by block, to avoid effects of slow shifts in data
582 'identity', 0, ...
583 'copycond', 0, ...
584 'copysubj', 0, ...
585 'replacefile', 1); % Replace
586 % Process: Compute covariance (noise or data) [Run02]
587 bst_process('CallProcess', 'process_noisecov', sFilesEpochs2, [], ...
588 'baseline', [-0.1, -0.0017], ...
589 'datatimewindow', [0, 0.5], ...
590 'sensortypes', 'MEG, EEG, SEEG, ECOG', ...
591 'target', 2, ... % Data covariance (covariance over data time window)
592 'dcoffset', 1, ... % Block by block, to avoid effects of slow shifts in data
593 'identity', 0, ...
594 'copycond', 0, ...
595 'copysubj', 0, ...
596 'replacefile', 1); % Replace
597 % Process: Snapshot: Data covariance
598 bst_process('CallProcess', 'process_snapshot', [sFilesEpochs1(1), sFilesEpochs2(1)], [], ...
599 'target', 12, ... % Data covariance
600 'Comment', 'Data covariance');
601
602
603
604 %% ===== TUTORIAL #22: SOURCE ESTIMATION =============================================
605 % ===================================================================================
606 disp([10 'DEMO> Tutorial #22: Source estimation' 10]);
607 % === GET DEVIANT AVERAGE RUN01 ===
608 % Process: Select recordings in: Subject01/S01_AEF_20131218_01_600Hz_notch
609 sFiles01 = bst_process('CallProcess', 'process_select_files_data', [], [], ...
610 'subjectname', SubjectName, ...
611 'condition', 'S01_AEF_20131218_01_600Hz_notch', ...
612 'includebad', 0);
613 % Process: Select file comments with tag: deviant
614 sFilesAvgDeviant01 = bst_process('CallProcess', 'process_select_tag', sFiles01, [], ...
615 'tag', 'Avg: deviant', ...
616 'search', 2, ... % Search the file comments
617 'select', 1); % Select only the files with the tag
618
619 % === CONSTRAINED EXAMPLE ===
620 % Minimum norm options
621 InverseOptions = struct(...
622 'Comment', 'MN: MEG', ...
623 'InverseMethod', 'minnorm', ...
624 'InverseMeasure', 'amplitude', ...
625 'SourceOrient', {{'fixed'}}, ...
626 'Loose', 0.2, ...
627 'UseDepth', 1, ...
628 'WeightExp', 0.5, ...
629 'WeightLimit', 10, ...
630 'NoiseMethod', 'reg', ...
631 'NoiseReg', 0.1, ...
632 'SnrMethod', 'fixed', ...
633 'SnrRms', 0.001, ...
634 'SnrFixed', 3, ...
635 'ComputeKernel', 1, ...
636 'DataTypes', {{'MEG'}});
637 % Process: Compute sources [2018]
638 sFilesSrcDeviant01 = bst_process('CallProcess', 'process_inverse_2018', sFilesAvgDeviant01, [], ...
639 'output', 2, ... % Kernel only: one per file
640 'inverse', InverseOptions);
641
642 % === DISPLAY SOURCES MANUALLY ===
643 % View time series
644 hFigSrc1 = view_timeseries(sFilesAvgDeviant01(1).FileName, 'MEG');
645 % View on the cortex surface
646 hFigSrc2 = script_view_sources(sFilesSrcDeviant01.FileName, 'cortex');
647 % Set current time to 90ms
648 panel_time('SetCurrentTime', 0.090);
649 % Set orientation
650 figure_3d('SetStandardView', hFigSrc2, 'left');
651 % Set surface threshold
652 iSurf = 1;
653 thresh = .30;
654 panel_surface('SetDataThreshold', hFigSrc2, iSurf, thresh);
655 % Set surface smoothing
656 panel_surface('SetSurfaceSmooth', hFigSrc2, iSurf, .6, 0);
657 % Show sulci
658 panel_surface('SetShowSulci', hFigSrc2, iSurf, 1);
659
660 % View sources on MRI (3D orthogonal slices)
661 hFigSrc3 = script_view_sources(sFilesSrcDeviant01.FileName, 'mri3d');
662 panel_surface('SetDataThreshold', hFigSrc3, iSurf, thresh);
663 % Set the position of the cuts in the 3D figure
664 cutsPosVox = [74 93 159];
665 panel_surface('PlotMri', hFigSrc3, cutsPosVox);
666
667 % View sources with MRI Viewer
668 hFigSrc4 = script_view_sources(sFilesSrcDeviant01.FileName, 'mriviewer');
669 panel_surface('SetDataThreshold', hFigSrc4, iSurf, thresh);
670 % Set the position of the cuts in the MRI Viewer (values in millimeters)
671 figure_mri('SetLocation', 'voxel', hFigSrc4, [], cutsPosVox);
672 % Close figures
673 close([hFigSrc1 hFigSrc2 hFigSrc3 hFigSrc4]);
674
675 % === UNCONSTRAINED EXAMPLE ===
676 % Unconstrained minnorm
677 InverseOptions.Comment = 'MN: MEG';
678 InverseOptions.InverseMeasure = 'amplitude';
679 InverseOptions.SourceOrient = {'free'};
680 % Process: Compute sources [2018]
681 sFilesSrcUnconst = bst_process('CallProcess', 'process_inverse_2018', sFilesAvgDeviant01, [], ...
682 'output', 2, ... % Kernel only: one per file
683 'inverse', InverseOptions);
684
685
686 % === NORMALIZED SOURCES ===
687 % dSPM
688 InverseOptions.Comment = 'dSPM: MEG';
689 InverseOptions.InverseMeasure = 'dspm2018';
690 InverseOptions.SourceOrient = {'fixed'};
691 sFilesSrcDspm = bst_process('CallProcess', 'process_inverse_2018', sFilesAvgDeviant01, [], ...
692 'output', 2, ... % Kernel only: one per file
693 'inverse', InverseOptions);
694 % sLORETA (old function)
695 sFilesSrcSloreta = bst_process('CallProcess', 'process_inverse', sFilesAvgDeviant01, [], ...
696 'comment', '', ...
697 'method', 3, ... % sLORETA
698 'wmne', struct(...
699 'SourceOrient', {{'fixed'}}, ...
700 'loose', 0.2, ...
701 'SNR', 3, ...
702 'pca', 1, ...
703 'diagnoise', 0, ...
704 'regnoise', 1, ...
705 'magreg', 0.1, ...
706 'gradreg', 0.1, ...
707 'depth', 1, ...
708 'weightexp', 0.5, ...
709 'weightlimit', 10), ...
710 'sensortypes', 'MEG, MEG MAG, MEG GRAD, EEG', ...
711 'output', 2); % Kernel only: one per file
712 % Process: Z-score normalization: [-100ms,-2ms]
713 sFilesSrcZscore = bst_process('CallProcess', 'process_baseline_norm', sFilesSrcDeviant01, [], ...
714 'baseline', [-0.100, -0.002], ...
715 'source_abs', 0, ...
716 'method', 'zscore'); % Z-score transformation: x_std = (x - μ) / σ
717
718 % Process: Snapshot: Sources (one time)
719 bst_process('CallProcess', 'process_snapshot', sFilesSrcDeviant01, [], ...
720 'target', 8, ... % Sources (one time)
721 'orient', 1, ... % left
722 'time', 0.09, ...
723 'threshold', 30, ...
724 'Comment', 'Current density map (Constrained)');
725 bst_process('CallProcess', 'process_snapshot', sFilesSrcDspm, [], ...
726 'target', 8, ... % Sources (one time)
727 'orient', 1, ... % left
728 'time', 0.09, ...
729 'threshold', 60, ...
730 'Comment', 'dSPM');
731 bst_process('CallProcess', 'process_snapshot', sFilesSrcSloreta, [], ...
732 'target', 8, ... % Sources (one time)
733 'orient', 1, ... % left
734 'time', 0.09, ...
735 'threshold', 60, ...
736 'Comment', 'sLORETA');
737 bst_process('CallProcess', 'process_snapshot', sFilesSrcZscore, [], ...
738 'target', 8, ... % Sources (one time)
739 'orient', 1, ... % left
740 'time', 0.09, ...
741 'threshold', 60, ...
742 'Comment', 'Z-score');
743 bst_process('CallProcess', 'process_snapshot', sFilesSrcUnconst, [], ...
744 'target', 8, ... % Sources (one time)
745 'orient', 1, ... % left
746 'time', 0.0917, ...
747 'threshold', 0, ...
748 'Comment', 'Current density map (Unconstrained)');
749
750 % === DELETE EXPERIMENTS ===
751 % Process: Delete constrained example
752 bst_process('CallProcess', 'process_delete', [sFilesSrcDeviant01, sFilesSrcDspm, sFilesSrcSloreta, sFilesSrcZscore, sFilesSrcUnconst], [], ...
753 'target', 1); % Delete selected files
754
755
756 % === SHARED KERNEL ===
757 % Constrained minnorm
758 InverseOptions.Comment = 'MN: MEG';
759 InverseOptions.InverseMeasure = 'amplitude';
760 InverseOptions.SourceOrient = {'fixed'};
761 % Process: Compute sources [2018]
762 sFilesAvgSrc = bst_process('CallProcess', 'process_inverse_2018', sFilesAvg, [], ...
763 'output', 1, ... % Kernel only: shared
764 'inverse', InverseOptions);
765
766
767 % === AVERAGE SOURCES ACROSS RUNS ===
768 % Process: Average: By trial group (subject average)
769 sFilesIntraSrc = bst_process('CallProcess', 'process_average', sFilesAvgSrc, [], ...
770 'avgtype', 6, ... % By trial group (subject average)
771 'avg_func', 1, ... % Arithmetic average: mean(x)
772 'weighted', 1, ...
773 'scalenormalized', 0);
774 % Process: Low-pass:40Hz
775 sFilesIntraSrcLow = bst_process('CallProcess', 'process_bandpass', sFilesIntraSrc, [], ...
776 'highpass', 0, ...
777 'lowpass', 40, ...
778 'attenuation', 'strict', ... % 60dB
779 'mirror', 0, ...
780 'overwrite', 0);
781 % Process: Z-score normalization: [-100ms,-2ms]
782 sFilesIntraZscore = bst_process('CallProcess', 'process_baseline_norm', sFilesIntraSrcLow, [], ...
783 'baseline', [-0.100, -0.0017], ...
784 'source_abs', 0, ...
785 'method', 'zscore'); % Z-score transformation: x_std = (x - μ) / σ
786
787 % Process: Delete intermediate results
788 bst_process('CallProcess', 'process_delete', sFilesIntraSrcLow, [], ...
789 'target', 1); % Delete selected files
790 % Screen captures
791 bst_process('CallProcess', 'process_snapshot', sFilesIntraZscore, [], ...
792 'target', 8, ... % Sources (one time)
793 'orient', 1, ... % left
794 'time', 0.09, ...
795 'threshold', 40, ...
796 'Comment', 'Average across runs (left)');
797 bst_process('CallProcess', 'process_snapshot', sFilesIntraZscore, [], ...
798 'target', 8, ... % Sources (one time)
799 'orient', 2, ... % right
800 'time', 0.09, ...
801 'threshold', 40, ...
802 'Comment', 'Average across runs (right)');
803 bst_process('CallProcess', 'process_snapshot', sFilesIntraZscore(1), [], ...
804 'target', 9, ... % Sources (contact sheet)
805 'orient', 1, ... % left
806 'contact_time', [0, 0.35], ...
807 'contact_nimage', 15, ...
808 'threshold', 20, ...
809 'Comment', 'Average across runs');
810
811
812 %% ===== TUTORIAL #23: SCOUTS ========================================================
813 % ===================================================================================
814 disp([10 'DEMO> Tutorial #23: Scouts' 10]);
815 % Load surface file
816 sCortex = in_tess_bst(CortexFile);
817 % Add new scouts in first atlas
818 sCortex.iAtlas = find(strcmpi({sCortex.Atlas.Name}, 'Destrieux'));
819 % Save file
820 bst_save(file_fullpath(CortexFile), sCortex, 'v7');
821 % Unload everything
822 bst_memory('UnloadAll', 'Forced');
823 % Find scouts indices to display: {'A1L', 'A1R', 'IFGL', 'M1L'}
824 [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'});
825
826 % View cortex
827 hFigSurf1 = view_surface(CortexFile, [], [], 'NewFigure');
828 hFigSurf2 = view_surface(CortexFile, [], [], 'NewFigure');
829 figure_3d('SetStandardView', hFigSurf1, 'left');
830 figure_3d('SetStandardView', hFigSurf2, 'right');
831 panel_surface('SetSurfaceSmooth', hFigSurf1, 1, .6, 0);
832 panel_surface('SetSurfaceSmooth', hFigSurf2, 1, .6, 0);
833 panel_surface('SetShowSulci', hFigSurf1, 1, 1);
834 panel_surface('SetShowSulci', hFigSurf2, 1, 1);
835 % Configure scouts display
836 panel_scout('SetScoutsOptions', 0, 1, 1, 'all', 0.7, 1, 1, 0);
837 % View scouts
838 hFigScouts = view_scouts({sFilesIntraZscore.FileName}, iScouts);
839 hLegend = findobj(hFigScouts, 'Type', 'legend');
840 if ~isempty(hLegend) && ishandle(hLegend(1))
841 set(hLegend(1), 'Units', 'pixels');
842 pos = get(hLegend(1), 'Position');
843 set(hLegend(1), 'Position', [1, 1, pos(3), pos(4)]);
844 end
845 % Save figures
846 bst_report('Snapshot', hFigScouts, sFilesIntraZscore(1).FileName, 'Scouts', [100 100 670 250]);
847 % Close all
848 pause(1);
849 bst_memory('UnloadAll', 'Forced');
850
851
852
853 %% ===== TUTORIAL #24: TIME-FREQUENCY ================================================
854 % ===================================================================================
855 disp([10 'DEMO> Tutorial #24: Time-frequency' 10]);
856 % Process: Simulate generic signals
857 sSim = bst_process('CallProcess', 'process_simulate_matrix', [], [], ...
858 'subjectname', 'Test', ...
859 'condition', 'Simulation', ...
860 'samples', 6000, ...
861 'srate', 1000, ...
862 '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);']);
863
864 % Time-frequency options
865 TfOptions = struct(...
866 'Comment', 'Power,1-60Hz', ...
867 'TimeBands', [], ...
868 '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], ...
869 'MorletFc', 1, ...
870 'MorletFwhmTc', 3, ...
871 'ClusterFuncTime', 'none', ...
872 'Measure', 'power', ...
873 'Output', 'average', ...
874 'SaveKernel', 0);
875 % Process: Time-frequency (Morlet wavelets)
876 sSimTf1 = bst_process('CallProcess', 'process_timefreq', sSim, [], ...
877 'edit', TfOptions, ...
878 'normalize', 'multiply'); % 1/f compensation: Multiply output values by frequency
879
880 % === NORMALIZATION ===
881 % Process: Time-frequency (Morlet wavelets)
882 sSimTf2 = bst_process('CallProcess', 'process_timefreq', sSim, [], ...
883 'edit', TfOptions, ...
884 'normalize', 'none'); % None: Save non-standardized time-frequency maps
885 % Process: Spectral flattening
886 sSimTf2Multi = bst_process('CallProcess', 'process_tf_norm', sSimTf2, [], ...
887 'normalize', 'multiply', ... % 1/f compensation (multiple by frequency)
888 'overwrite', 0);
889 % Process: Event-related perturbation (ERS/ERD): [750ms,1250ms]
890 sSimTf2Ersd = bst_process('CallProcess', 'process_baseline_norm', sSimTf2, [], ...
891 'baseline', [0.75, 1.25], ...
892 'method', 'ersd', ... % Event-related perturbation (ERS/ERD): x_std = (x - μ) / μ * 100
893 'overwrite', 0);
894
895 % Process: Snapshot: Time-frequency maps
896 bst_process('CallProcess', 'process_snapshot', sSimTf2, [], ...
897 'target', 14, ... % Time-frequency maps
898 'Comment', 'Not normalized');
899 % Process: Snapshot: Time-frequency maps
900 bst_process('CallProcess', 'process_snapshot', sSimTf2Multi, [], ...
901 'target', 14, ... % Time-frequency maps
902 'Comment', 'Spectral flattening: 1/f compensation');
903 % Process: Snapshot: Time-frequency maps
904 bst_process('CallProcess', 'process_snapshot', sSimTf2Ersd, [], ...
905 'target', 14, ... % Time-frequency maps
906 'Comment', 'ERS/ERD');
907 % Spectrum/Time series
908 hFigTf1 = view_spectrum(sSimTf2.FileName, 'Spectrum');
909 hFigTf2 = view_spectrum(sSimTf2.FileName, 'TimeSeries');
910 panel_time('SetCurrentTime', 0.5);
911 panel_freq('SetCurrentFreq', 2, 0);
912 bst_report('Snapshot', [hFigTf1 hFigTf2], sSimTf2.FileName, 'Not normalized: 2s/20Hz', [200, 200, 400, 250]);
913 panel_time('SetCurrentTime', 2.02);
914 panel_freq('SetCurrentFreq', 20, 0);
915 bst_report('Snapshot', [hFigTf1 hFigTf2], sSimTf2.FileName, 'Not normalized: 2s/20Hz', [200, 200, 400, 250]);
916 bst_memory('UnloadAll', 'Forced');
917
918
919 % === HILBERT TRANSFORM ===
920 % Process: Hilbert transform
921 sSimHilbert = bst_process('CallProcess', 'process_hilbert', sSim, [], ...
922 'edit', struct(...
923 'Comment', 'Power', ...
924 'TimeBands', [], ...
925 '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'}}, ...
926 'ClusterFuncTime', 'none', ...
927 'Measure', 'power', ...
928 'Output', 'all', ...
929 'SaveKernel', 0), ...
930 'normalize', 'none', ... % None: Save non-standardized time-frequency maps
931 'mirror', 0);
932 % Process: Spectral flattening
933 sSimHilbertMulti = bst_process('CallProcess', 'process_tf_norm', sSimHilbert, [], ...
934 'normalize', 'multiply', ... % 1/f compensation (multiple by frequency)
935 'overwrite', 0);
936 % Process: Event-related perturbation (ERS/ERD): [750ms,1250ms]
937 sSimHilbertErsd = bst_process('CallProcess', 'process_baseline_norm', sSimHilbert, [], ...
938 'baseline', [0.75, 1.25], ...
939 'method', 'ersd', ... % Event-related perturbation (ERS/ERD): x_std = (x - μ) / μ * 100
940 'overwrite', 0);
941
942 % Process: Snapshot: Time-frequency maps
943 bst_process('CallProcess', 'process_snapshot', sSimHilbert, [], ...
944 'target', 14, ... % Time-frequency maps
945 'Comment', 'Not normalized');
946 % Process: Snapshot: Time-frequency maps
947 bst_process('CallProcess', 'process_snapshot', sSimHilbertMulti, [], ...
948 'target', 14, ... % Time-frequency maps
949 'Comment', 'Spectral flattening: 1/f compensation');
950 % Process: Snapshot: Time-frequency maps
951 bst_process('CallProcess', 'process_snapshot', sSimHilbertErsd, [], ...
952 'target', 14, ... % Time-frequency maps
953 'Comment', 'ERS/ERD');
954
955 % === SINGLE TRIALS ===
956 TfOptions.Comment = 'Avg,Power,1-150Hz';
957 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];
958 % Process: Time-frequency (Morlet wavelets)
959 sEpochsAvgTf = bst_process('CallProcess', 'process_timefreq', sFilesEpochs1, [], ...
960 'sensortypes', 'MEG, EEG', ...
961 'edit', TfOptions, ...
962 'normalize', 'none'); % None: Save non-standardized time-frequency maps
963 % Process: Event-related perturbation (ERS/ERD): [-75ms,0ms]
964 sEpochsAvgTfErsd = bst_process('CallProcess', 'process_baseline_norm', sEpochsAvgTf, [], ...
965 'baseline', [-0.075, 0], ...
966 'method', 'ersd', ... % Event-related perturbation (ERS/ERD): x_std = (x - μ) / μ * 100
967 'overwrite', 0);
968
969 % === DISPLAY ===
970 % View time-frequency file
971 hFigTf1 = view_timefreq(sEpochsAvgTfErsd.FileName, 'SingleSensor');
972 % Configure display
973 sOptions = panel_display('GetDisplayOptions');
974 sOptions.HideEdgeEffects = 1;
975 sOptions.HighResolution = 1;
976 panel_display('SetDisplayOptions', sOptions);
977 % Other display modes
978 hFigTf2 = view_timefreq(sEpochsAvgTfErsd.FileName, 'AllSensors');
979 hFigTf3 = view_timefreq(sEpochsAvgTfErsd.FileName, '2DLayout');
980 hFigTf4 = view_timefreq(sEpochsAvgTfErsd.FileName, '2DLayoutOpt');
981 bst_colormaps('SetColormapName', 'stat2', 'jet');
982 bst_colormaps('SetColormapAbsolute', 'stat2', 1);
983 bst_report('Snapshot', hFigTf1, sEpochsAvgTfErsd.FileName, 'Time-frequency', [200, 200, 400, 250]);
984 bst_report('Snapshot', [hFigTf2 hFigTf3 hFigTf4], sEpochsAvgTfErsd.FileName, 'Time-frequency', [200, 200, 750, 400]);
985 close([hFigTf1 hFigTf2 hFigTf3 hFigTf4]);
986 % Image [channel x time]
987 hFigTf5 = view_erpimage(sEpochsAvgTfErsd.FileName, 'trialimage');
988 % Topographies
989 hFigTf6 = view_topography(sEpochsAvgTfErsd.FileName, 'MEG', '3DSensorCap');
990 hFigTf7 = view_topography(sEpochsAvgTfErsd.FileName, 'MEG', '2DDisc');
991 hFigTf8 = view_topography(sEpochsAvgTfErsd.FileName, 'MEG', '2DSensorCap');
992 hFigTf9 = view_topography(sEpochsAvgTfErsd.FileName, 'MEG', '2DLayout');
993 panel_time('SetCurrentTime', 0.175);
994 panel_freq('SetCurrentFreq', 8, 0);
995 bst_report('Snapshot', [hFigTf5 hFigTf6 hFigTf7 hFigTf8 hFigTf9], sEpochsAvgTfErsd.FileName, 'Time-frequency: 8Hz', [200, 200, 400, 250]);
996 close([hFigTf5 hFigTf6 hFigTf7 hFigTf8 hFigTf9]);
997
998
999 % === AVERAGE FOR SCOUTS ===
1000 % Select all sources for the single deviant epochs
1001 sFilesEpochDeviantSrc = bst_process('CallProcess', 'process_select_files_results', [], [], ...
1002 'subjectname', SubjectName, ...
1003 'condition', '', ...
1004 'includebad', 0);
1005 sFilesEpochDeviantSrc = bst_process('CallProcess', 'process_select_tag', sFilesEpochDeviantSrc, [], ...
1006 'tag', 'deviant', ...
1007 'search', 1, ... % Search the file names
1008 'select', 1); % Select only the files with the tag
1009 sFilesEpochDeviantSrc = bst_process('CallProcess', 'process_select_tag', sFilesEpochDeviantSrc, [], ...
1010 'tag', 'average', ...
1011 'search', 1, ... % Search the file names
1012 'select', 2); % Exclude the files with the tag
1013
1014 % Process: Time-frequency (Morlet wavelets)
1015 sFilesTfScout = bst_process('CallProcess', 'process_timefreq', sFilesEpochDeviantSrc, [], ...
1016 'clusters', {'Destrieux', {'G_temp_sup-G_T_transv L', 'G_temp_sup-G_T_transv R', 'G_front_inf-Opercular L', 'G_precentral L'}}, ...
1017 'scoutfunc', 1, ... % Mean
1018 'edit', struct(...
1019 'Comment', 'Deviant: Scouts,Avg,Power,1-150Hz', ...
1020 'TimeBands', [], ...
1021 '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], ...
1022 'MorletFc', 1, ...
1023 'MorletFwhmTc', 3, ...
1024 'ClusterFuncTime', 'after', ...
1025 'Measure', 'power', ...
1026 'Output', 'average', ...
1027 'SaveKernel', 0), ...
1028 'normalize', 'none'); % None: Save non-standardized time-frequency maps)
1029 % Process: Event-related perturbation (ERS/ERD): [-75ms,0ms]
1030 sFilesTfScoutErsd = bst_process('CallProcess', 'process_baseline_norm', sFilesTfScout, [], ...
1031 'baseline', [-0.075, 0], ...
1032 'method', 'ersd', ... % Event-related perturbation (ERS/ERD): x_std = (x - μ) / μ * 100
1033 'overwrite', 0);
1034 % Process: Snapshot: Time-frequency maps
1035 bst_process('CallProcess', 'process_snapshot', sFilesTfScoutErsd, [], ...
1036 'target', 14, ... % Time-frequency maps
1037 'Comment', 'ERS/ERD');
1038
1039
1040 % === FULL CORTEX / HILBERT ===
1041 % Process: Hilbert transform
1042 sFilesHilbertCortex = bst_process('CallProcess', 'process_hilbert', sFilesEpochDeviantSrc, [], ...
1043 'clusters', {}, ...
1044 'scoutfunc', 1, ... % Mean
1045 'edit', struct(...
1046 'Comment', 'Deviant: Avg,Magnitude', ...
1047 'TimeBands', [], ...
1048 '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'}}, ...
1049 'ClusterFuncTime', 'none', ...
1050 'Measure', 'power', ...
1051 'Output', 'average', ...
1052 'RemoveEvoked', 0, ...
1053 'SaveKernel', 0), ...
1054 'normalize', 'none', ... % None: Save non-standardized time-frequency maps
1055 'mirror', 0);
1056 % Process: Event-related perturbation (ERS/ERD): [-75ms,0ms]
1057 sFilesHilbertCortexErsd = bst_process('CallProcess', 'process_baseline_norm', sFilesHilbertCortex, [], ...
1058 'baseline', [-0.075, 0], ...
1059 'method', 'ersd', ... % Event-related perturbation (ERS/ERD): x_std = (x - μ) / μ * 100
1060 'overwrite', 0);
1061
1062 % View results
1063 hFigTf1 = view_surface_data([], sFilesHilbertCortexErsd.FileName);
1064 hFigTf2 = view_timefreq(sFilesHilbertCortexErsd.FileName, 'SingleSensor', 362);
1065 figure_3d('SetStandardView', hFigTf1, 'left');
1066 panel_surface('SetDataThreshold', hFigTf1, 1, 0.5);
1067 panel_time('SetCurrentTime', 0.175);
1068 panel_freq('SetCurrentFreq', 3);
1069 bst_colormaps('RestoreDefaults', 'stat2');
1070 bst_report('Snapshot', [hFigTf1 hFigTf2], sFilesHilbertCortexErsd.FileName, 'Hilbert transform: Alpha band', [200, 200, 400, 250]);
1071 bst_memory('UnloadAll', 'Forced');
1072
1073
1074 %% ===== TUTORIAL #25: DIFFRERENCE ===================================================
1075 % ===================================================================================
1076 disp([10 'DEMO> Tutorial #25: Difference' 10]);
1077
1078 % ===== SELECT TRIALS (DATA) =====
1079 % Process: Select recordings in: Subject01/*
1080 sFilesAll = bst_process('CallProcess', 'process_select_files_data', [], [], ...
1081 'subjectname', SubjectName, ...
1082 'condition', '', ...
1083 'includebad', 0);
1084 % Process: Select file names with tag: deviant_trial
1085 sEpochDeviant = bst_process('CallProcess', 'process_select_tag', sFilesAll, [], ...
1086 'tag', 'deviant_trial', ...
1087 'search', 1, ... % Search the file names
1088 'select', 1); % Select only the files with the tag
1089 % Process: Select file names with tag: standard_trial
1090 sEpochStandard = bst_process('CallProcess', 'process_select_tag', sFilesAll, [], ...
1091 'tag', 'standard_trial', ...
1092 'search', 1, ... % Search the file names
1093 'select', 1); % Select only the files with the tag
1094
1095 % ===== SELECT TRIALS (SOURCE) =====
1096 % Process: Select recordings in: Subject01/*
1097 sFilesAllSrc = bst_process('CallProcess', 'process_select_files_results', [], [], ...
1098 'subjectname', SubjectName, ...
1099 'condition', '', ...
1100 'includebad', 0);
1101 % Process: Select file names with tag: deviant_trial
1102 sEpochDeviantSrc = bst_process('CallProcess', 'process_select_tag', sFilesAllSrc, [], ...
1103 'tag', 'deviant_trial', ...
1104 'search', 1, ... % Search the file names
1105 'select', 1); % Select only the files with the tag
1106 % Process: Select file names with tag: standard_trial
1107 sEpochStandardSrc = bst_process('CallProcess', 'process_select_tag', sFilesAllSrc, [], ...
1108 'tag', 'standard_trial', ...
1109 'search', 1, ... % Search the file names
1110 'select', 1); % Select only the files with the tag
1111
1112 % ===== ABSOLUTE DIFFERENCE ======
1113 % Process: Difference: A-B, abs
1114 sDiffSrc = bst_process('CallProcess', 'process_diff_ab', sFilesIntraSrc(1).FileName, sFilesIntraSrc(2).FileName, ...
1115 'source_abs', 1);
1116 % Process: Set comment: deviant|abs - standard|abs
1117 sDiffSrc = bst_process('CallProcess', 'process_set_comment', sDiffSrc, [], ...
1118 'tag', 'deviant|abs - standard|abs', ...
1119 'isindex', 1);
1120 % Process: Low-pass:40Hz
1121 sDiffSrcZscore = bst_process('CallProcess', 'process_bandpass', sDiffSrc, [], ...
1122 'highpass', 0, ...
1123 'lowpass', 40, ...
1124 'attenuation', 'strict', ... % 60dB
1125 'mirror', 0, ...
1126 'overwrite', 1);
1127 % Process: Z-score transformation: [-100ms,-2ms]
1128 sDiffSrcZscore = bst_process('CallProcess', 'process_baseline_norm', sDiffSrcZscore, [], ...
1129 'baseline', [-0.1, -0.002], ...
1130 'source_abs', 0, ...
1131 'method', 'zscore', ... % Z-score transformation: x_std = (x - μ) / σ
1132 'overwrite', 0);
1133 % Process: Snapshot: Sources (contact sheet)
1134 bst_process('CallProcess', 'process_snapshot', sDiffSrcZscore, [], ...
1135 'target', 9, ... % Sources (contact sheet)
1136 'modality', 1, ... % MEG (All)
1137 'orient', 1, ... % left
1138 'contact_time', [0, 0.35], ...
1139 'contact_nimage', 15, ...
1140 'threshold', 30, ...
1141 'Comment', 'Difference deviant - standard (absolute)');
1142
1143 % ===== RELATIVE DIFFERENCE =====
1144 % Process: Difference: A-B
1145 sDiffSrcRel = bst_process('CallProcess', 'process_diff_ab', sFilesIntraSrc(1).FileName, sFilesIntraSrc(2).FileName, ...
1146 'source_abs', 0);
1147 % Process: Set comment: deviant - standard
1148 sDiffSrcRel = bst_process('CallProcess', 'process_set_comment', sDiffSrcRel, [], ...
1149 'tag', 'deviant - standard', ...
1150 'isindex', 1);
1151 % Process: Low-pass:40Hz
1152 sDiffSrcRelZscore = bst_process('CallProcess', 'process_bandpass', sDiffSrcRel, [], ...
1153 'highpass', 0, ...
1154 'lowpass', 40, ...
1155 'attenuation', 'strict', ... % 60dB
1156 'mirror', 0, ...
1157 'overwrite', 1);
1158 % Process: Z-score transformation: [-100ms,-2ms]
1159 sDiffSrcRelZscore = bst_process('CallProcess', 'process_baseline_norm', sDiffSrcRelZscore, [], ...
1160 'baseline', [-0.1, -0.002], ...
1161 'source_abs', 0, ...
1162 'method', 'zscore', ... % Z-score transformation: x_std = (x - μ) / σ
1163 'overwrite', 0);
1164 % Configure colormap: hot/absolute
1165 bst_colormaps('SetColormapName', 'stat2', 'hot');
1166 bst_colormaps('SetColormapAbsolute', 'stat2', 1);
1167 % Process: Snapshot: Sources (contact sheet)
1168 bst_process('CallProcess', 'process_snapshot', sDiffSrcRelZscore, [], ...
1169 'target', 9, ... % Sources (contact sheet)
1170 'modality', 1, ... % MEG (All)
1171 'orient', 1, ... % left
1172 'contact_time', [0, 0.35], ...
1173 'contact_nimage', 15, ...
1174 'threshold', 30, ...
1175 'Comment', 'Difference deviant - standard (relative)');
1176 % Restore colormap: rwb/relative
1177 bst_colormaps('SetColormapName', 'stat2', 'cmap_rbw');
1178 bst_colormaps('SetColormapAbsolute', 'stat2', 0);
1179
1180 % ===== DIFFERENCE OF MEANS =====
1181 % Process: Select uniform number of files [uniform]
1182 [sEpochDeviantUni, sEpochStandardUni] = bst_process('CallProcess', 'process_select_uniform2', sEpochDeviant, sEpochStandard, ...
1183 'nfiles', 0, ...
1184 'method', 4); % Uniformly distributed
1185 % Process: Difference of means [mean]
1186 sDiffMean = bst_process('CallProcess', 'process_diff_mean', sEpochDeviantUni, sEpochStandardUni, ...
1187 'avg_func', 1, ... % Arithmetic average mean(A) - mean(B)
1188 'weighted', 0);
1189 % Process: Snapshot: Recordings time series
1190 bst_process('CallProcess', 'process_snapshot', sDiffMean, [], ...
1191 'target', 5, ... % Recordings time series
1192 'modality', 1, ... % MEG (All)
1193 'Comment', 'Difference of means');
1194
1195
1196
1197 %% ===== TUTORIAL #26: STATISTICS ====================================================
1198 % ===================================================================================
1199 disp([10 'DEMO> Tutorial #26: Statistics' 10]);
1200 % ===== HISTOGRAMS =====
1201 % Process: Extract values: [160ms] MLP57
1202 sHistoDeviant = bst_process('CallProcess', 'process_extract_values', sEpochDeviant, [], ...
1203 'timewindow', [0.16, 0.16], ...
1204 'sensortypes', 'MLP57', ...
1205 'isabs', 0, ...
1206 'avgtime', 0, ...
1207 'avgrow', 0, ...
1208 'dim', 2, ... % Concatenate time (dimension 2)
1209 'Comment', '');
1210 % Process: Extract values: [160ms] MLP57
1211 sHistoStandard = bst_process('CallProcess', 'process_extract_values', sEpochStandard, [], ...
1212 'timewindow', [0.16, 0.16], ...
1213 'sensortypes', 'MLP57', ...
1214 'isabs', 0, ...
1215 'avgtime', 0, ...
1216 'avgrow', 0, ...
1217 'dim', 2, ... % Concatenate time (dimension 2)
1218 'Comment', '');
1219 % Display histograms
1220 hFigHisto = view_histogram({sHistoDeviant.FileName, sHistoStandard.FileName});
1221 bst_report('Snapshot', hFigHisto, sHistoDeviant.FileName, 'Histograms for MLP57/160ms');
1222 close(hFigHisto);
1223
1224 % ===== EXEMPLE #1: PARAMETRIC/DATA =====
1225 % Process: t-test [equal] [-100ms,500ms] H0:(A-B = 0)
1226 sTestParamData = bst_process('CallProcess', 'process_test_parametric2', sEpochDeviant, sEpochStandard, ...
1227 'timewindow', [-0.1, 0.5], ...
1228 'sensortypes', '', ...
1229 'isabs', 0, ...
1230 'avgtime', 0, ...
1231 'avgrow', 0, ...
1232 'Comment', '', ...
1233 '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
1234 'tail', 'two'); % Two-tailed
1235 % Set display properties
1236 StatThreshOptions = bst_get('StatThreshOptions');
1237 StatThreshOptions.pThreshold = 0.05;
1238 StatThreshOptions.Correction = 'fdr';
1239 StatThreshOptions.Control = [1 2 3];
1240 bst_set('StatThreshOptions', StatThreshOptions);
1241 % Process: Snapshot: Recordings time series
1242 bst_process('CallProcess', 'process_snapshot', sTestParamData, [], ...
1243 'target', 5, ... % Recordings time series
1244 'modality', 1, ... % MEG (All)
1245 'time', 0.16, ...
1246 'Comment', 'Parametric t-test (p<0.05, FDR)');
1247 % Process: Snapshot: Recordings topography (one time)
1248 bst_process('CallProcess', 'process_snapshot', sTestParamData, [], ...
1249 'target', 6, ... % Recordings topography (one time)
1250 'modality', 1, ... % MEG (All)
1251 'time', 0.16, ...
1252 'Comment', 'Parametric t-test (p<0.05, FDR)');
1253
1254 % ===== EXEMPLE #2: NON-PARAMETRIC/DATA =====
1255 % Process: Perm t-test equal [-100ms,500ms MEG] H0:(A=B), H1:(A<>B)
1256 sTestPermData = bst_process('CallProcess', 'process_test_permutation2', sEpochDeviant, sEpochStandard, ...
1257 'timewindow', [-0.1, 0.5], ...
1258 'sensortypes', 'MEG', ...
1259 'isabs', 0, ...
1260 'avgtime', 0, ...
1261 'avgrow', 0, ...
1262 'iszerobad', 1, ...
1263 'Comment', '', ...
1264 '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))
1265 'randomizations', 1000, ...
1266 'tail', 'two'); % Two-tailed
1267 % Process: Snapshot: Recordings time series
1268 bst_process('CallProcess', 'process_snapshot', sTestPermData, [], ...
1269 'target', 5, ... % Recordings time series
1270 'modality', 1, ... % MEG (All)
1271 'time', 0.16, ...
1272 'Comment', 'Non-parametric t-test (p<0.05, FDR)');
1273 % Process: Snapshot: Recordings topography (one time)
1274 bst_process('CallProcess', 'process_snapshot', sTestPermData, [], ...
1275 'target', 6, ... % Recordings topography (one time)
1276 'modality', 1, ... % MEG (All)
1277 'time', 0.16, ...
1278 'Comment', 'Non-parametric t-test (p<0.05, FDR)');
1279
1280 % ===== EXEMPLE #3: CLUSTER/DATA =====
1281 % Process: FT t-test unequal cluster [-100ms,500ms MEG] H0:(A=B), H1:(A<>B)
1282 sTestClustData = bst_process('CallProcess', 'process_ft_timelockstatistics', sEpochDeviant, sEpochStandard, ...
1283 'sensortypes', 'MEG', ...
1284 'timewindow', [-0.1, 0.5], ...
1285 'isabs', 0, ...
1286 'avgtime', 0, ...
1287 'avgchan', 0, ...
1288 'randomizations', 1000, ...
1289 'statistictype', 1, ... % Independent t-test
1290 'tail', 'two', ... % Two-tailed
1291 'correctiontype', 2, ... % cluster
1292 'minnbchan', 0, ...
1293 'clusteralpha', 0.05);
1294 % Process: Snapshot: Recordings time series
1295 bst_process('CallProcess', 'process_snapshot', sTestClustData, [], ...
1296 'target', 5, ... % Recordings time series
1297 'time', 0.16, ...
1298 'modality', 1, ... % MEG (All)
1299 'Comment', 'Cluster-based permutation test');
1300 % Process: Snapshot: Recordings topography (one time)
1301 bst_process('CallProcess', 'process_snapshot', sTestClustData, [], ...
1302 'target', 6, ... % Recordings topography (one time)
1303 'modality', 1, ... % MEG (All)
1304 'time', 0.16, ...
1305 'Comment', 'Cluster-based permutation test');
1306
1307 % ===== EXAMPLE #4: PARAMETRIC/SOURCES =====
1308 % Process: t-test [equal] [-100ms,500ms] H0:(A-B = 0)
1309 sTestParamSrc = bst_process('CallProcess', 'process_test_parametric2', sEpochDeviantSrc, sEpochStandardSrc, ...
1310 'timewindow', [-0.1, 0.5], ...
1311 'scoutsel', {}, ...
1312 'scoutfunc', 1, ... % Mean
1313 'isnorm', 0, ...
1314 'avgtime', 0, ...
1315 'Comment', '', ...
1316 '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
1317 'tail', 'two'); % Two-tailed
1318 % Process: Difference of means [abs(mean)]
1319 sDiffMeanSrc = bst_process('CallProcess', 'process_diff_mean', sEpochDeviantSrc, sEpochStandardSrc, ...
1320 'avg_func', 2, ... % Absolute value of average abs(mean(A)) - abs(mean(B))
1321 'weighted', 0);
1322 % Process: Apply statistic threshold: p<0.05 (FDR:1,2,3)
1323 sDiffMeanSrcThresh = bst_process('CallProcess', 'process_extract_pthresh2', sTestParamSrc, sDiffMeanSrc, ...
1324 'pthresh', 0.05, ...
1325 'correction', 3, ... % False discovery rate (FDR)
1326 'control1', 1, ...
1327 'control2', 1, ...
1328 'control3', 1);
1329 % Process: Snapshot: Sources (one time)
1330 bst_process('CallProcess', 'process_snapshot', sTestParamSrc, [], ...
1331 'target', 8, ... % Sources (one time)
1332 'orient', 1, ... % left
1333 'time', 0.148, ...
1334 'threshold', 40, ...
1335 'Comment', 'Parametric t-test (p<0.05, FDR)');
1336 % Process: Snapshot: Sources (one time)
1337 bst_process('CallProcess', 'process_snapshot', sDiffMeanSrc, [], ...
1338 'target', 8, ... % Sources (one time)
1339 'orient', 1, ... % left
1340 'time', 0.148, ...
1341 'threshold', 40, ...
1342 'Comment', 'abs(average(deviant)) - abs(average(standard))');
1343 % Process: Snapshot: Sources (one time)
1344 bst_process('CallProcess', 'process_snapshot', sDiffMeanSrcThresh, [], ...
1345 'target', 8, ... % Sources (one time)
1346 'orient', 1, ... % left
1347 'time', 0.148, ...
1348 'threshold', 0, ...
1349 'Comment', 'Different of mean thresholded with t-test results');
1350
1351 % ===== EXAMPLE #5: PARAMETRIC/SCOUTS =====
1352 % Process: t-test equal [-100ms,500ms] H0:(A=B), H1:(A<>B)
1353 sTestParamScout = bst_process('CallProcess', 'process_test_parametric2', sEpochDeviantSrc, sEpochStandardSrc, ...
1354 'timewindow', [-0.1, 0.5], ...
1355 'scoutsel', {'Destrieux', {'G_front_inf-Opercular L', 'G_precentral L', 'G_temp_sup-G_T_transv L'}}, ...
1356 'scoutfunc', 1, ... % Mean
1357 'isnorm', 0, ...
1358 'avgtime', 0, ...
1359 'Comment', '', ...
1360 '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
1361 'tail', 'two'); % Two-tailed
1362 % Process: Apply statistic threshold: p<0.05 (FDR:1,2,3)
1363 sTestParamScoutThresh = bst_process('CallProcess', 'process_extract_pthresh', sTestParamScout, [], ...
1364 'pthresh', 0.05, ...
1365 'correction', 3, ... % False discovery rate (FDR)
1366 'control1', 1, ...
1367 'control2', 1, ...
1368 'control3', 1);
1369 % Process: Compute head model
1370 bst_process('CallProcess', 'process_headmodel', sTestParamScoutThresh, [], ...
1371 'sourcespace', 1, ... % Cortex surface
1372 'meg', 3); % Overlapping spheres
1373 % Process: Simulate recordings from scouts
1374 sSimulData = bst_process('CallProcess', 'process_simulate_recordings', sTestParamScoutThresh, [], ...
1375 'scouts', {'Destrieux', {'G_front_inf-Opercular L', 'G_precentral L', 'G_temp_sup-G_T_transv L'}}, ...
1376 'savesources', 1);
1377
1378 % Get corresponding source file
1379 [sStudy,iStudy,iRes] = bst_get('ResultsForDataFile', sSimulData.FileName);
1380 sSimulSrc = sStudy.Result(iRes).FileName;
1381 % Reset visualization filters
1382 panel_filter('SetFilters', 0, [], 0, [], 0, [], 0, 0);
1383 % Process: Snapshot: Recordings time series
1384 bst_process('CallProcess', 'process_snapshot', sTestParamScout, [], ...
1385 'target', 5, ... % Recordings time series
1386 'time', 0.148, ...
1387 'Comment', 'Parametric t-test (p<0.05, FDR)');
1388 % Process: Snapshot: Sources (one time)
1389 bst_process('CallProcess', 'process_snapshot', sSimulSrc, [], ...
1390 'target', 8, ... % Sources (one time)
1391 'orient', 1, ... % left
1392 'time', 0.148, ...
1393 'threshold', 0, ...
1394 'Comment', 'Simulated sources');
1395 % Process: Snapshot: Recordings time series
1396 bst_process('CallProcess', 'process_snapshot', sSimulData, [], ...
1397 'target', 5, ... % Recordings time series
1398 'modality', 1, ... % MEG (All)
1399 'time', 0.148, ...
1400 'Comment', 'Simulated MEG recordings');
1401
1402
1403 % ===== EXAMPLE #6: NON-PARAMETRIC/TIMEFREQ =====
1404 TfOptions.Output = 'all';
1405 % Process: Time-frequency (Morlet wavelets) / DEVIANT
1406 sEpochDeviantTf = bst_process('CallProcess', 'process_timefreq', sEpochDeviant, [], ...
1407 'sensortypes', 'MLP57', ...
1408 'edit', TfOptions, ...
1409 'normalize', 'none'); % None: Save non-standardized time-frequency maps
1410 % Process: Time-frequency (Morlet wavelets) / STANDARD
1411 sEpochStandardTf = bst_process('CallProcess', 'process_timefreq', sEpochStandard, [], ...
1412 'sensortypes', 'MLP57', ...
1413 'edit', TfOptions, ...
1414 'normalize', 'none'); % None: Save non-standardized time-frequency maps
1415 % Process: Perm t-test equal [-100ms,500ms 1-150Hz] H0:(A=B), H1:(A<>B)
1416 sTestTf = bst_process('CallProcess', 'process_test_permutation2', sEpochDeviantTf, sEpochStandardTf, ...
1417 'timewindow', [-0.1, 0.5], ...
1418 'freqrange', [1, 150], ...
1419 'rows', '', ...
1420 'isabs', 0, ...
1421 'avgtime', 0, ...
1422 'avgrow', 0, ...
1423 'avgfreq', 0, ...
1424 'matchrows', 0, ...
1425 'iszerobad', 1, ...
1426 'Comment', '', ...
1427 '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))
1428 'randomizations', 1000, ...
1429 'tail', 'two'); % Two-tailed
1430 % Set stat threshold
1431 StatThreshOptions.pThreshold = 0.05;
1432 StatThreshOptions.Correction = 'none';
1433 bst_set('StatThreshOptions', StatThreshOptions);
1434 % Process: Snapshot: Time-frequency maps
1435 bst_process('CallProcess', 'process_snapshot', sTestTf, [], ...
1436 'target', 14, ... % Time-frequency maps
1437 'Comment', 'Non-parametric t-test (p<0.05, Uncorrected)');
1438 % Process: Delete intermediate results
1439 bst_process('CallProcess', 'process_delete', [sEpochDeviantTf, sEpochStandardTf], [], ...
1440 'target', 1); % Delete selected files
1441
1442
1443
1444 %% ===== SAVE REPORT =====
1445 % Save and display report
1446 ReportFile = bst_report('Save', []);
1447 if ~isempty(reports_dir) && ~isempty(ReportFile)
1448 bst_report('Export', ReportFile, reports_dir);
1449 else
1450 bst_report('Open', ReportFile);
1451 end
1452
1453 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
1 function tutorial_visual_single(bids_dir, reports_dir)
2 % TUTORIAL_VISUAL_SINGLE: Runs the Brainstorm/SPM group analysis pipeline (single subject, BIDS version).
3 %
4 % ONLINE TUTORIALS: https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle
5 %
6 % INPUTS:
7 % - bids_dir: Path to folder ds000117 (https://openneuro.org/datasets/ds000117)
8 % |- derivatives/freesurfer/sub-XX : Segmentation folders generated with FreeSurfer
9 % |- derivatives/meg_derivatives/sub-XX/ses-meg/meg/*.fif : MEG+EEG recordings (processed with MaxFilter's SSS)
10 % |- derivatives/meg_derivatives/sub-emptyroom/ses-meg/meg/*.fif : Empty room measurements
11 % - reports_dir: If defined, exports all the reports as HTML to this folder
12
13 % @=============================================================================
14 % This function is part of the Brainstorm software:
15 % https://neuroimage.usc.edu/brainstorm
16 %
17 % Copyright (c) University of Southern California & McGill University
18 % This software is distributed under the terms of the GNU General Public License
19 % as published by the Free Software Foundation. Further details on the GPLv3
20 % license can be found at http://www.gnu.org/copyleft/gpl.html.
21 %
22 % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
23 % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
24 % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
25 % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
26 % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
27 %
28 % For more information type "brainstorm license" at command prompt.
29 % =============================================================================@
30 %
31 % Author: Francois Tadel, Elizabeth Bock, 2016-2018
32
33
34 %% ===== SCRIPT VARIABLES =====
35 % Full list of subjects to process
36 SubjectNames = {'sub-01', 'sub-02', 'sub-03', 'sub-04', 'sub-05', 'sub-06', 'sub-07', 'sub-08', ...
37 'sub-09', 'sub-10', 'sub-11', 'sub-12', 'sub-13', 'sub-14', 'sub-15', 'sub-16'};
38 % Empty-room dates for each subject (so that we can match automatically recordings with empty-room)
39 EmptyRoomSubj = 'sub-emptyroom';
40 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', ...
41 '15-May-2009', '15-May-2009', '01-Jun-2009', '01-Jun-2009', '01-Jun-2009', '26-Nov-2009', '08-Dec-2009', '08-Dec-2009'};
42 % Bad channels {iSubj} = {Run01, Run02, Run03, Run04, Run05, Run06}
43 BadChannels{1} = {'EEG016', 'EEG070', 'EEG050',{'EEG008','EEG050'}, [], []};
44 BadChannels{2} = {{'EEG027', 'EEG030', 'EEG038'}, 'EEG010', 'EEG010', 'EEG010', 'EEG010', 'EEG010'};
45 BadChannels{3} = {{'EEG008','EEG017'}, {'EEG008','EEG017'}, {'EEG008','EEG017'}, {'EEG008','EEG017'}, {'EEG008','EEG017','EEG001'}, {'EEG008','EEG017','EEG020'}};
46 BadChannels{4} = {{'EEG038'}, {'EEG038','EEG001','EEG016'}, {'EEG038','EEG001','EEG016'}, {'EEG038','EEG001'}, {'EEG038','EEG001','EEG016'}, {'EEG038','EEG001','EEG016'}};
47 BadChannels{5} = {'EEG001', 'EEG001', [], [], [], []};
48 BadChannels{6} = {'EEG068', [], 'EEG004', [], [], []};
49 BadChannels{7} = {[], [], {'EEG004','EEG008'}, {'EEG004','EEG008'},{'EEG004','EEG008','EEG043','EEG045','EEG047'}, {'EEG004','EEG008'}};
50 BadChannels{8} = {[], [], [], [], [], []};
51 BadChannels{9} = {[], 'EEG004', 'EEG004', [], 'EEG004', 'EEG004'};
52 BadChannels{10} = {[], [], [], [], [], []};
53 BadChannels{11} = {{'EEG010','EEG050'}, 'EEG050', 'EEG050', 'EEG050', 'EEG050', 'EEG050'};
54 BadChannels{12} = {{'EEG024','EEG057'}, {'EEG024','EEG057'}, {'EEG024','EEG057'}, {'EEG024','EEG057','EEG070'}, {'EEG024','EEG057'}, {'EEG024','EEG057','EEG070'}};
55 BadChannels{13} = {'EEG009', 'EEG009', {'EEG009','EEG057','EEG69'}, 'EEG009', {'EEG009','EEG044'}, {'EEG009','EEG044'}};
56 BadChannels{14} = {'EEG029', 'EEG029', 'EEG029', {'EEG004','EEG008','EEG016','EEG029'}, {'EEG004','EEG008','EEG016','EEG029'}, {'EEG004','EEG008','EEG016','EEG029'}};
57 BadChannels{15} = {'EEG038', 'EEG038', 'EEG038', 'EEG038', {'EEG054','EEG038'}, 'EEG038'};
58 BadChannels{16} = {'EEG008', 'EEG008', 'EEG008', 'EEG008', 'EEG008', 'EEG008'};
59 % SSP components to remove {iSubj} = {sRun01, sRun02, sRun03, sRun03, sRun04, sRun05, sRun06}, sRun0X={ECG_GRAD,ECG_MAG}
60 SspSelect{1} = {{1,1}, {1,1}, {1,1}, {1,1}, {1,1}, {1,1}};
61 SspSelect{2} = {{1,1}, {1,1}, {1,1}, {1,1}, {3,1}, {1,1}};
62 SspSelect{3} = {{[],1}, {1,1}, {1,1}, {1,1}, {1,1}, {1,1}};
63 SspSelect{4} = {{[],1}, {[],1}, {[],1}, {[],1}, {[],1}, {[],1}};
64 SspSelect{5} = {{2,1}, {1,1}, {1,1}, {[],1}, {1,1}, {1,1}};
65 SspSelect{6} = {{2,1}, {2,1}, {1,1}, {2,1}, {1,1}, {2,1}};
66 SspSelect{7} = {{1,1}, {1,1}, {1,1}, {1,1}, {1,1}, {1,1}};
67 SspSelect{8} = {{1,1}, {1,1}, {[],1}, {2,1}, {1,1}, {2,1}};
68 SspSelect{9} = {{1,1}, {1,1}, {[],1}, {[],1}, {1,1}, {1,1}};
69 SspSelect{10} = {{1,1}, {1,1}, {1,1}, {1,1}, {1,1}, {1,1}};
70 SspSelect{11} = {{[],1}, {[],1}, {[],1}, {[],1}, {[],[]}, {[],[]}};
71 SspSelect{12} = {{[1,2],[1,2]}, {1,1}, {1,1}, {1,1}, {1,1}, {1,1}};
72 SspSelect{13} = {{[],[]}, {[],[]}, {[],[]}, {[],[]}, {[],[]}, {[],[]}};
73 SspSelect{14} = {{1,1}, {1,1}, {1,1}, {1,1}, {1,1}, {1,1}};
74 SspSelect{15} = {{1,1}, {1,1}, {1,1}, {1,1}, {1,1}, {1,1}};
75 SspSelect{16} = {{1,1}, {1,1}, {1,1}, {2,1}, {1,1}, {1,1}};
76
77
78 %% ===== CREATE PROTOCOL =====
79 % Start brainstorm without the GUI
80 if ~brainstorm('status')
81 brainstorm nogui
82 end
83 % Output folder for reports
84 if (nargin < 2) || isempty(reports_dir) || ~isdir(reports_dir)
85 reports_dir = [];
86 end
87 % You have to specify the folder in which the tutorial dataset is unzipped
88 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'))
89 error('The first argument must be the full path to the tutorial folder.');
90 end
91 % The protocol name has to be a valid folder name (no spaces, no weird characters...)
92 ProtocolName = 'TutorialVisual';
93 % Delete existing protocol
94 gui_brainstorm('DeleteProtocol', ProtocolName);
95 % Create new protocol
96 gui_brainstorm('CreateProtocol', ProtocolName, 0, 0);
97 % Set visualization filters: 40Hz low-pass, no high-pass
98 panel_filter('SetFilters', 1, 40, 0, [], 0, [], 0, 0);
99 % Set colormap: local color scale
100 bst_colormaps('SetMaxMode', 'meg', 'local');
101 bst_colormaps('SetMaxMode', 'eeg', 'local');
102
103
104 %% ===== PRE-PROCESS AND IMPORT =====
105 for iSubj = 1:16
106 % Start a new report (one report per subject)
107 bst_report('Start');
108 disp(sprintf('\n===== IMPORT: SUBJECT #%d =====\n', iSubj));
109
110 % If subject already exists: delete it
111 [sSubject, iSubject] = bst_get('Subject', SubjectNames{iSubj});
112 if ~isempty(sSubject)
113 db_delete_subjects(iSubject);
114 end
115
116 % ===== FILES TO IMPORT =====
117 % Build the path of the files to import
118 AnatDir = fullfile(bids_dir, 'derivatives', 'freesurfer', SubjectNames{iSubj}, 'ses-mri', 'anat');
119 DataDir = fullfile(bids_dir, 'derivatives', 'meg_derivatives', SubjectNames{iSubj}, 'ses-meg', 'meg');
120 % Check if the folder contains the required files
121 if ~file_exist(AnatDir)
122 error(['The folder "' AnatDir '" does not exist.']);
123 end
124 if ~file_exist(DataDir)
125 error(['The folder "' DataDir '" does not exist.']);
126 end
127
128 % ===== ANATOMY =====
129 % Process: Import anatomy folder
130 bst_process('CallProcess', 'process_import_anatomy', [], [], ...
131 'subjectname', SubjectNames{iSubj}, ...
132 'mrifile', {AnatDir, 'FreeSurfer'}, ...
133 'nvertices', 15000);
134
135 % ===== PROCESS EACH RUN =====
136 for iRun = 1:6
137 % Files to import
138 FifFile = bst_fullfile(DataDir, sprintf('%s_ses-meg_task-facerecognition_run-%02d_proc-sss_meg.fif', SubjectNames{iSubj}, iRun));
139
140 % ===== LINK CONTINUOUS FILE =====
141 % Process: Create link to raw file
142 sFileRaw = bst_process('CallProcess', 'process_import_data_raw', [], [], ...
143 'subjectname', SubjectNames{iSubj}, ...
144 'datafile', {FifFile, 'FIF'}, ...
145 'channelreplace', 1, ...
146 'channelalign', 0);
147 % Set acquisition date
148 panel_record('SetAcquisitionDate', sFileRaw.iStudy, AcquisitionDates{iSubj});
149
150 % ===== PREPARE CHANNEL FILE =====
151 % Process: Set channels type
152 bst_process('CallProcess', 'process_channel_settype', sFileRaw, [], ...
153 'sensortypes', 'EEG061, EEG064', ...
154 'newtype', 'NOSIG');
155 bst_process('CallProcess', 'process_channel_settype', sFileRaw, [], ...
156 'sensortypes', 'EEG062', ...
157 'newtype', 'EOG');
158 bst_process('CallProcess', 'process_channel_settype', sFileRaw, [], ...
159 'sensortypes', 'EEG063', ...
160 'newtype', 'ECG');
161
162 % Process: Remove head points
163 sFileRaw = bst_process('CallProcess', 'process_headpoints_remove', sFileRaw, [], ...
164 'zlimit', 0);
165 % Process: Refine registration
166 sFileRaw = bst_process('CallProcess', 'process_headpoints_refine', sFileRaw, []);
167 % Process: Project electrodes on scalp
168 sFileRaw = bst_process('CallProcess', 'process_channel_project', sFileRaw, []);
169
170 % Process: Snapshot: Sensors/MRI registration
171 bst_process('CallProcess', 'process_snapshot', sFileRaw, [], ...
172 'target', 1, ... % Sensors/MRI registration
173 'modality', 1, ... % MEG (All)
174 'orient', 1, ... % left
175 'Comment', sprintf('MEG/MRI Registration: Subject #%d, Run #%d', iSubj, iRun));
176 bst_process('CallProcess', 'process_snapshot', sFileRaw, [], ...
177 'target', 1, ... % Sensors/MRI registration
178 'modality', 4, ... % EEG
179 'orient', 1, ... % left
180 'Comment', sprintf('EEG/MRI Registration: Subject #%d, Run #%d', iSubj, iRun));
181
182 % ===== IMPORT TRIGGERS =====
183 % Process: Read from channel
184 bst_process('CallProcess', 'process_evt_read', sFileRaw, [], ...
185 'stimchan', 'STI101', ...
186 'trackmode', 2, ... % Bit: detect the changes for each bit independently
187 'zero', 0);
188 % Process: Group by name
189 bst_process('CallProcess', 'process_evt_groupname', sFileRaw, [], ...
190 'combine', 'Unfamiliar=3,4', ...
191 'dt', 0, ...
192 'delete', 1);
193 % Process: Rename event
194 bst_process('CallProcess', 'process_evt_rename', sFileRaw, [], ...
195 'src', '3', ...
196 'dest', 'Famous');
197 % Process: Rename event
198 bst_process('CallProcess', 'process_evt_rename', sFileRaw, [], ...
199 'src', '5', ...
200 'dest', 'Scrambled');
201 % Process: Add time offset
202 bst_process('CallProcess', 'process_evt_timeoffset', sFileRaw, [], ...
203 'info', [], ...
204 'eventname', 'Famous, Unfamiliar, Scrambled', ...
205 'offset', 0.0345);
206 % Process: Delete events
207 bst_process('CallProcess', 'process_evt_delete', sFileRaw, [], ...
208 'eventname', '1,2,6,7,8,9,10,11,12,13,14,15,16');
209 % Process: Detect cHPI activity (Elekta):STI201
210 bst_process('CallProcess', 'process_evt_detect_chpi', sFileRaw, [], ...
211 'eventname', 'chpi_bad', ...
212 'channelname', 'STI201', ...
213 'method', 'off'); % Mark as bad when the HPI coils are OFF
214
215 % ===== FREQUENCY FILTERS =====
216 % Process: Notch filter: 50Hz 100Hz 150Hz 200Hz
217 sFileClean = bst_process('CallProcess', 'process_notch', sFileRaw, [], ...
218 'freqlist', [50, 100, 150, 200], ...
219 'sensortypes', 'MEG, EEG', ...
220 'read_all', 0);
221 % Process: Power spectrum density (Welch)
222 sFilesPsd = bst_process('CallProcess', 'process_psd', [sFileRaw, sFileClean], [], ...
223 'timewindow', [], ...
224 'win_length', 4, ...
225 'win_overlap', 50, ...
226 'sensortypes', 'MEG, EEG', ...
227 'edit', struct(...
228 'Comment', 'Power', ...
229 'TimeBands', [], ...
230 'Freqs', [], ...
231 'ClusterFuncTime', 'none', ...
232 'Measure', 'power', ...
233 'Output', 'all', ...
234 'SaveKernel', 0));
235 % Process: Snapshot: Frequency spectrum
236 bst_process('CallProcess', 'process_snapshot', sFilesPsd, [], ...
237 'target', 10, ... % Frequency spectrum
238 'Comment', sprintf('Power spctrum: Subject #%d, Run #%d', iSubj, iRun));
239
240 % ===== BAD CHANNELS =====
241 if ~isempty(BadChannels{iSubj}{iRun})
242 % Process: Set bad channels
243 bst_process('CallProcess', 'process_channel_setbad', sFileClean, [], ...
244 'sensortypes', BadChannels{iSubj}{iRun});
245 end
246
247 % ===== EEG REFERENCE =====
248 % Process: Re-reference EEG
249 bst_process('CallProcess', 'process_eegref', sFileClean, [], ...
250 'eegref', 'AVERAGE', ...
251 'sensortypes', 'EEG');
252
253 % ===== DETECT ARTIFACTS ======
254 % Process: Detect heartbeats
255 bst_process('CallProcess', 'process_evt_detect_ecg', sFileClean, [], ...
256 'channelname', 'EEG063', ...
257 'timewindow', [], ...
258 'eventname', 'cardiac');
259 % Different amplitude thresholds for different subjects
260 if strcmpi(SubjectNames{iSubj}, 'sub-05')
261 thresholdMAX = 50;
262 else
263 thresholdMAX = 100;
264 end
265 % Process: Detect: blink_BAD - Detects all events where the amplitude exceeds 100uV
266 bst_process('CallProcess', 'process_evt_detect_threshold', sFileClean, [], ...
267 'eventname', 'blink_BAD', ...
268 'channelname', 'EEG062', ...
269 'timewindow', [], ...
270 'thresholdMAX', thresholdMAX, ...
271 'units', 3, ... % uV (10^-6)
272 'bandpass', [0.3, 20], ...
273 'isAbsolute', 1, ...
274 'isDCremove', 0);
275
276 % ===== SSP COMPUTATION =====
277 % Process: SSP ECG: cardiac
278 bst_process('CallProcess', 'process_ssp_ecg', sFileClean, [], ...
279 'eventname', 'cardiac', ...
280 'sensortypes', 'MEG GRAD', ...
281 'usessp', 1, ...
282 'select', SspSelect{iSubj}{iRun}{1});
283 bst_process('CallProcess', 'process_ssp_ecg', sFileClean, [], ...
284 'eventname', 'cardiac', ...
285 'sensortypes', 'MEG MAG', ...
286 'usessp', 1, ...
287 'select', SspSelect{iSubj}{iRun}{2});
288 % Process: Snapshot: SSP projectors
289 bst_process('CallProcess', 'process_snapshot', sFileClean, [], ...
290 'target', 2, ...
291 'Comment', sprintf('Subject #%d, Run #%d', iSubj, iRun)); % SSP projectors
292
293 % ===== IMPORT BAD EVENTS =====
294 % Get bad segments: this is typically done manually, not from a script
295 BadSegments = GetBadSegments(iSubj, iRun);
296 % Process: Import from file
297 bst_process('CallProcess', 'process_evt_import', sFileClean, [], ...
298 'evtfile', {BadSegments, 'ARRAY-TIMES'}, ...
299 'evtname', 'BAD');
300
301 % ===== IMPORT TRIALS =====
302 % Process: Import MEG/EEG: Events
303 sFilesEpochs = bst_process('CallProcess', 'process_import_data_event', sFileClean, [], ...
304 'subjectname', SubjectNames{iSubj}, ...
305 'condition', '', ...
306 'eventname', 'Famous, Scrambled, Unfamiliar', ...
307 'timewindow', [], ...
308 'epochtime', [-0.5, 1.2], ...
309 'createcond', 0, ...
310 'ignoreshort', 1, ...
311 'usectfcomp', 1, ...
312 'usessp', 1, ...
313 'freq', [], ...
314 'baseline', [-0.5, -0.0009]);
315
316 % ===== AVERAGE: RUN =====
317 % Process: Average: By trial group (folder average)
318 sFilesAvg = bst_process('CallProcess', 'process_average', sFilesEpochs, [], ...
319 'avgtype', 5, ... % By trial group (folder average)
320 'avg_func', 1, ... % Arithmetic average: mean(x)
321 'weighted', 0, ...
322 'keepevents', 0);
323 % Process: Snapshot: Recordings time series
324 bst_process('CallProcess', 'process_snapshot', sFilesAvg, [], ...
325 'target', 5, ... % Recordings time series
326 'modality', 4, ... % EEG
327 'time', 0.11, ...
328 'Comment', sprintf('Subject #%d, Run #%d', iSubj, iRun));
329 % Process: Snapshot: Recordings topography
330 bst_process('CallProcess', 'process_snapshot', sFilesAvg, [], ...
331 'target', 6, ... % Recordings topography (one time)
332 'modality', 4, ... % EEG
333 'time', 0.11, ...
334 'Comment', sprintf('Subject #%d, Run #%d', iSubj, iRun));
335
336 % ===== COMPUTE NOISECOV: EEG =====
337 % Process: Compute covariance (noise or data)
338 bst_process('CallProcess', 'process_noisecov', sFilesEpochs, [], ...
339 'baseline', [-0.5, -0.0009], ...
340 'sensortypes', 'EEG', ...
341 'target', 1, ... % Noise covariance (covariance over baseline time window)
342 'dcoffset', 1, ... % Block by block, to avoid effects of slow shifts in data
343 'identity', 0, ...
344 'copycond', 0, ...
345 'copysubj', 0, ...
346 'replacefile', 1); % Replace
347 end
348
349 % Save report
350 ReportFile = bst_report('Save', []);
351 if ~isempty(reports_dir) && ~isempty(ReportFile)
352 bst_report('Export', ReportFile, bst_fullfile(reports_dir, ['report_' ProtocolName '_' SubjectNames{iSubj} '.html']));
353 end
354 end
355
356
357 %% ===== EMPTY ROOM RECORDINGS =====
358 disp(sprintf('\n===== IMPORT: EMPTY-ROOM =====\n'));
359 % Loop on all the noise sessions
360 NoiseFiles = {};
361 for ses = {'20090409', '20090506', '20090511', '20090515', '20090518', '20090601', '20091126', '20091208'}
362 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']);
363 end
364 % Process: Create link to raw file
365 sFilesNoise = bst_process('CallProcess', 'process_import_data_raw', [], [], ...
366 'subjectname', EmptyRoomSubj, ...
367 'datafile', {NoiseFiles, 'FIF'}, ...
368 'channelreplace', 1, ...
369 'channelalign', 0);
370 % Process: Notch filter: 50Hz 100Hz 150Hz 200Hz
371 sFileNoiseClean = bst_process('CallProcess', 'process_notch', sFilesNoise, [], ...
372 'freqlist', [50, 100, 150, 200], ...
373 'sensortypes', 'MEG, EEG', ...
374 'read_all', 0);
375 % Process: Compute noise covariance
376 bst_process('CallProcess', 'process_noisecov', sFileNoiseClean, [], ...
377 'baseline', [], ...
378 'sensortypes', 'MEG', ...
379 'target', 1, ... % Noise covariance (covariance over baseline time window)
380 'dcoffset', 1, ... % Block by block, to avoid effects of slow shifts in data
381 'identity', 0, ...
382 'copycond', 1, ...
383 'copysubj', 1, ...
384 'copymatch', 1, ...
385 'replacefile', 2); % Merge
386
387
388 %% ===== SOURCE ESTIMATION =====
389 % Start a new report (one report for the source estimation of all the subjects)
390 bst_report('Start');
391 % Loop on the subjects: This loop is separated from the previous one, because we should
392 % compute the BEM surfaces after importing all the runs, so that the registration is done
393 % using the high resolution head surface, instead of the smooth scalp BEM layer.
394 for iSubj = 1:length(SubjectNames)
395 disp(sprintf('\n===== SOURCES: SUBJECT #%d =====\n', iSubj));
396
397 % ===== BEM SURFACES =====
398 % Process: Generate BEM surfaces
399 bst_process('CallProcess', 'process_generate_bem', [], [], ...
400 'subjectname', SubjectNames{iSubj}, ...
401 'nscalp', 1082, ...
402 'nouter', 642, ...
403 'ninner', 642, ...
404 'thickness', 4);
405
406 % ===== SELECT ALL AVERAGES =====
407 % Process: Select data files in: */*
408 sFilesAvg = bst_process('CallProcess', 'process_select_files_data', [], [], ...
409 'subjectname', SubjectNames{iSubj});
410 % Process: Select file comments with tag: Avg
411 sFilesAvg = bst_process('CallProcess', 'process_select_tag', sFilesAvg, [], ...
412 'tag', 'Avg'); % Select only the files with the tag
413
414 % ===== COMPUTE HEAD MODELS =====
415 % Process: Compute head model (only for the first run of the subject)
416 bst_process('CallProcess', 'process_headmodel', sFilesAvg(1), [], ...
417 'sourcespace', 1, ... % Cortex surface
418 'meg', 3, ... % Overlapping spheres
419 'eeg', 3, ... % OpenMEEG BEM
420 'ecog', 1, ... %
421 'seeg', 1, ... %
422 'openmeeg', struct(...
423 'BemSelect', [1, 1, 1], ...
424 'BemCond', [1, 0.0125, 1], ...
425 'BemNames', {{'Scalp', 'Skull', 'Brain'}}, ...
426 'BemFiles', {{}}, ...
427 'isAdjoint', 0, ...
428 'isAdaptative', 1, ...
429 'isSplit', 0, ...
430 'SplitLength', 4000));
431 % Get all the runs for this subject (ie the list of the study indices)
432 iStudyOther = setdiff(unique([sFilesAvg.iStudy]), sFilesAvg(1).iStudy);
433 % Copy the forward model file to the other runs
434 sHeadmodel = bst_get('HeadModelForStudy', sFilesAvg(1).iStudy);
435 for iStudy = iStudyOther
436 db_add(iStudy, sHeadmodel.FileName);
437 end
438
439 % ===== COMPUTE SOURCES: MEG =====
440 % Process: Compute sources [2018]
441 sAvgSrcMeg = bst_process('CallProcess', 'process_inverse_2018', sFilesAvg, [], ...
442 'output', 1, ... % Kernel only: shared
443 'inverse', struct(...
444 'Comment', 'MN: MEG ALL', ...
445 'InverseMethod', 'minnorm', ...
446 'InverseMeasure', 'amplitude', ...
447 'SourceOrient', {{'fixed'}}, ...
448 'Loose', 0.2, ...
449 'UseDepth', 1, ...
450 'WeightExp', 0.5, ...
451 'WeightLimit', 10, ...
452 'NoiseMethod', 'reg', ...
453 'NoiseReg', 0.1, ...
454 'SnrMethod', 'fixed', ...
455 'SnrRms', 1e-06, ...
456 'SnrFixed', 3, ...
457 'ComputeKernel', 1, ...
458 'DataTypes', {{'MEG GRAD', 'MEG MAG'}}));
459 % Process: Snapshot: Sources (one time) - Loop only to get a correct comment for the report
460 for i = 1:length(sAvgSrcMeg)
461 bst_process('CallProcess', 'process_snapshot', sAvgSrcMeg(i), [], ...
462 'target', 8, ... % Sources (one time)
463 'orient', 4, ... % bottom
464 'time', 0.11, ...
465 'threshold', 20, ...
466 'Comment', ['MEG sources: ' sFilesAvg(i).FileName]);
467 end
468
469 % ===== COMPUTE SOURCES: EEG =====
470 % Process: Compute sources [2018]
471 sAvgSrcEeg = bst_process('CallProcess', 'process_inverse_2018', sFilesAvg, [], ...
472 'output', 1, ... % Kernel only: shared
473 'inverse', struct(...
474 'Comment', 'MN: EEG', ...
475 'InverseMethod', 'minnorm', ...
476 'InverseMeasure', 'amplitude', ...
477 'SourceOrient', {{'fixed'}}, ...
478 'Loose', 0.2, ...
479 'UseDepth', 1, ...
480 'WeightExp', 0.5, ...
481 'WeightLimit', 10, ...
482 'NoiseMethod', 'reg', ...
483 'NoiseReg', 0.1, ...
484 'SnrMethod', 'fixed', ...
485 'SnrRms', 1e-06, ...
486 'SnrFixed', 3, ...
487 'ComputeKernel', 1, ...
488 'DataTypes', {{'EEG'}}));
489 % Process: Snapshot: Sources (one time) - Loop only to get a correct comment for the report
490 for i = 1:length(sAvgSrcEeg)
491 bst_process('CallProcess', 'process_snapshot', sAvgSrcEeg(i), [], ...
492 'target', 8, ... % Sources (one time)
493 'orient', 4, ... % bottom
494 'time', 0.11, ...
495 'threshold', 10, ...
496 'Comment', ['EEG sources: ' sFilesAvg(i).FileName]);
497 end
498 end
499 % Save report
500 ReportFile = bst_report('Save', []);
501 if ~isempty(reports_dir) && ~isempty(ReportFile)
502 bst_report('Export', ReportFile, bst_fullfile(reports_dir, ['report_' ProtocolName '_sources.html']));
503 end
504
505
506 %% ===== TIME-FREQUENCY =====
507 % Start a new report (one report for the time-frequency of all the subjects)
508 bst_report('Start');
509 % List of conditions to process separately
510 AllConditions = {'Famous', 'Scrambled', 'Unfamiliar'};
511 % Channels to display in the screen capture, by order of preference (if the first channel is bad, use the following)
512 SelChannel = {'EEG070','EEG060','EEG065','EEG050','EEG003'};
513 % Compute one separate time-frequency average for each subject/run/condition
514 for iSubj = 1:length(SubjectNames)
515 disp(sprintf('\n===== TIME-FREQUENCY: SUBJECT #%d =====\n', iSubj));
516 for iRun = 1:6
517 % Process: Select data files in: Subject/Run
518 sTrialsAll = bst_process('CallProcess', 'process_select_files_data', [], [], ...
519 'subjectname', SubjectNames{iSubj}, ...
520 'condition', sprintf('sub-%02d_ses-meg_task-facerecognition_run-%02d_proc-sss_meg_notch', iSubj, iRun));
521 % Loop on the conditions
522 for iCond = 1:length(AllConditions)
523 % Comment describing this average
524 strComment = [SubjectNames{iSubj}, ' / ', sprintf('run_%02d', iRun), ' / ', AllConditions{iCond}];
525 disp(['BST> ' strComment]);
526 % Find the first good channel in the display list
527 if isempty(BadChannels{iSubj}{iRun})
528 iSel = 1;
529 else
530 iSel = find(~ismember(SelChannel,BadChannels{iSubj}{iRun}), 1);
531 end
532 % Process: Select file comments with tag: Avg
533 sTrialsCond = bst_process('CallProcess', 'process_select_tag', sTrialsAll, [], ...
534 'tag', [AllConditions{iCond}, '_trial'], ...
535 'search', 1, ... % Search the file names
536 'select', 1); % Select only the files with the tag
537 % Process: Time-frequency (Morlet wavelets), averaged across trials
538 sTimefreq = bst_process('CallProcess', 'process_timefreq', sTrialsCond, [], ...
539 'sensortypes', 'MEG MAG, EEG', ...
540 'edit', struct(...
541 'Comment', ['Avg: ' AllConditions{iCond} ', Power, 6-60Hz'], ...
542 'TimeBands', [], ...
543 '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], ...
544 'MorletFc', 1, ...
545 'MorletFwhmTc', 3, ...
546 'ClusterFuncTime', 'none', ...
547 'Measure', 'power', ...
548 'Output', 'average', ...
549 'RemoveEvoked', 0, ...
550 'SaveKernel', 0), ...
551 'normalize', 'none'); % None: Save non-standardized time-frequency maps
552 % Process: Extract time: [-200ms,900ms]
553 sTimefreq = bst_process('CallProcess', 'process_extract_time', sTimefreq, [], ...
554 'timewindow', [-0.2, 0.9], ...
555 'overwrite', 1);
556 % Screen capture of one sensor
557 hFigTf = view_timefreq(sTimefreq.FileName, 'SingleSensor', SelChannel{iSel});
558 bst_report('Snapshot', hFigTf, strComment, 'Time-frequency', [200, 200, 400, 250]);
559 close(hFigTf);
560 end
561 end
562 end
563 % Save report
564 ReportFile = bst_report('Save', []);
565 if ~isempty(reports_dir) && ~isempty(ReportFile)
566 bst_report('Export', ReportFile, bst_fullfile(reports_dir, ['report_' ProtocolName '_timefreq.html']));
567 end
568 end
569
570
571
572
573 %% ===== SUPPORT FUNCTIONS =====
574 function BadSeg = GetBadSegments(iSubj, iRun)
575 BadSegments{1} = {...
576 [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], ...
577 [84.791 85.166], ...
578 [79.183 80.167], ...
579 [64.309 65.185], ...
580 [90.958 91.167; 178.005 178.355; 293.282 295.919; 312.298 316.479; 353.835 357.716], ...
581 [60.292 66.802; 69.975 71.210; 105.233 107.586; 108.822 109.506; 376.225 376.325]};
582 BadSegments{2} = {...
583 [223.806 224.199; 279.772 279.895; 453.241 455.108; 692.423 692.593], ...
584 [65.298 66.194; 304.727 306.178; 399.165 400.732], ...
585 [203.141 205.085; 281.579 287.883; 420.395 421.128], ...
586 [387.118 388.229; 440.318 441.900; 554.825 558.744], ...
587 [71.000 80.999; 82.750 87.367; 149.528 149.667; 264.747 267.995; 368.415 371.973; 376.263 378.763; 398.334 401.551; 537.410 541.645], ...
588 [38.000 47.999; 47.825 50.046; 61.298 61.384; 249.653 253.379; 282.917 283.820; 286.135 287.616; 298.167 300.196; 328.254 329.511; 335.957 337.817; 478.277 480.707]};
589 BadSegments{3} = {...
590 [406.312 407.207; 727.055 728.714], ...
591 [84.894 85.156; 152.028 152.946; 297.835 298.915; 418.272 421.845; 554.084 554.794], ...
592 [73.758 74.159; 378.212 378.536; 406.065 407.099; 470.541 471.698; 488.900 491.168; 529.596 530.453], ...
593 [94.874 95.152; 317.385 321.374; 325.696 327.055; 439.220 439.829; 454.473 455.175; 486.196 486.829; 518.660 522.015; 524.400 525.249; 562.417 570.325], ...
594 [96.208 97.181; 98.942 99.096; 135.005 135.754; 143.990 144.599; 250.139 250.247; 300.459 300.559; 338.265 339.322; 545.913 546.067], ...
595 [91.415 92.156; 284.843 286.525; 297.886 298.404; 317.046 317.163; 332.698 332.791; 358.946 359.402; 428.405 428.775; 478.374 478.690; 549.866 550.128]};
596 BadSegments{4} = {...
597 [22.967 22.967; 50.036 50.098; 52.058 52.058; 156.653 156.653; 171.565 173.386; 239.544 242.105; 268.162 270.175; 268.992 268.992; 316.032 316.032; 338.283 339.000; 357.959 361.909; 370.871 370.871; 381.579 383.677; 437.731 437.731; 463.482 468.505; 476.135 479.838; 486.652 488.272; 504.860 508.999], ...
598 [309.493 311.707; 342.681 344.525; 354.019 357.321; 390.023 391.225; 393.926 395.855; 404.221 405.069; 432.522 435.932; 459.048 460.715; 471.763 478.529; 549.387 551.999; 591.087 594.143; 608.541 611.079; 624.847 626.615; 649.648 651.570], ...
599 [57.411 58.198; 88.346 88.955; 200.761 202.335; 227.016 227.688; 257.726 258.054; 356.798 359.005; 404.260 411.003], ...
600 [46.000 54.823; 61.000 70.332; 203.005 207.125; 275.875 278.121; 313.500 314.824; 337.973 338.636; 422.505 426.239], ...
601 [58.000 62.479; 78.250 85.166; 89.955 91.360; 116.322 117.888; 130.013 131.987; 149.509 150.489; 174.650 175.823; 182.030 183.334; 196.758 197.384; 204.458 204.697; 205.236 208.663; 311.028 316.383; 320.700 327.181; 332.437 335.354; 344.205 346.133; 374.208 374.865; 385.519 386.214; 441.942 444.241; 453.957 456.997; 486.039 487.004; 501.238 504.185; 512.962 514.675; 553.398 556.215], ...
602 [41.406 45.743; 58.681 59.144; 108.086 108.896; 140.633 143.750; 196.110 199.474; 210.778 210.971; 234.649 235.143; 258.081 259.632; 339.101 340.805; 390.277 390.609; 438.935 442.122; 528.221 534.031]};
603 BadSegments{5} = {...
604 [265.539 265.778; 266.334 266.495; 268.479 268.965; 367.428 367.636; 439.655 442.779; 453.497 453.853; 504.997 505.329; 519.513 519.683; 595.674 595.982; 602.000 602.463], ...
605 [121.113 121.499; 124.971 126.213; 253.735 254.075; 272.232 272.464; 272.895 273.104; 346.368 346.645; 368.812 369.052; 406.382 406.605; 452.920 453.113; 454.903 455.112; 507.655 507.840; 508.766 509.013; 584.853 585.030; 594.831 595.656; 597.261 602.249], ...
606 [37.251 37.497; 38.825 39.056; 40.615 41.849; 43.624 44.758; 53.333 53.641; 54.698 55.076; 57.668 59.196; 79.129 79.360; 81.475 81.714; 122.658 123.375; 284.787 285.296; 288.754 288.993; 345.790 346.022; 421.212 421.459; 481.428 482.207; 503.408 503.685; 504.272 504.449; 524.451 524.714; 526.913 531.499], ...
607 [87.322 88.178; 91.085 91.325; 95.121 95.491; 114.174 114.397; 129.874 130.113; 151.220 151.544; 281.689 281.959; 532.966 533.345], ...
608 [59.176 60.218; 74.854 75.317; 308.180 309.877; 380.705 381.059], ...
609 [182.382 183.245; 196.220 196.736; 276.018 276.327; 292.490 294.086; 370.755 370.847; 435.644 436.624; 467.535 468.460; 522.838 525.847]};
610 BadSegments{6} = {...
611 [141.690 142.424; 157.070 157.417; 355.138 356.025; 423.999 423.999; 424.999 424.999; 426.999 426.999; 427.999 427.999; 486.430 488.151; 493.999 493.999; 501.511 501.619; 501.549 501.549; 501.585 501.585; 502.999 502.999; 503.999 503.999; 540.999 540.999; 541.999 541.999; 555.999 555.999; 556.999 556.999; 561.999 561.999; 563.999 563.999; 564.999 564.999; 565.999 565.999; 567.999 567.999], ...
612 [64.898 65.161; 71.700 72.718; 226.185 226.740; 324.124 324.425; 329.062 329.301; 486.143 486.975], ...
613 [62.300 63.148; 266.254 266.639; 409.920 410.221], ...
614 [54.048 55.214; 330.893 331.255], ...
615 [185.616 186.495; 331.411 331.796; 386.843 387.028; 387.999 387.999; 389.999 389.999; 434.575 434.875; 519.802 519.995], ...
616 [44.720 45.167; 211.446 211.964; 368.955 369.172]};
617 BadSegments{7} = {...
618 [154.966 155.144; 551.639 551.855], ...
619 [88.774 89.167; 107.999 107.999; 109.999 109.999; 110.999 110.999; 112.999 112.999; 113.999 113.999; 114.999 114.999; 119.999 119.999; 121.999 121.999; 124.223 125.465; 137.011 138.871], ...
620 [81.627 82.136; 377.953 381.046], ...
621 [241.136 242.171; 543.849 544.196; 596.639 598.553; 600.227 601.075; 603.999 603.999; 605.999 605.999; 609.999 609.999; 611.305 612.809; 614.999 614.999; 615.803 616.937; 623.694 625.877; 653.999 653.999; 655.055 655.756; 663.999 663.999], ...
622 [68.852 69.481; 74.034 75.200; 78.426 78.600; 104.497 105.963; 253.951 254.034; 256.964 257.038; 257.915 258.048; 323.254 324.156; 365.880 368.131; 369.952 370.060; 371.728 372.999; 430.931 431.965; 535.521 542.999], ...
623 [70.271 71.205; 94.441 96.445; 98.613 99.126; 112.318 112.749; 131.686 132.265; 148.935 150.615; 161.120 161.600; 205.325 208.214; 215.035 215.863; 217.403 218.818; 286.178 287.171; 399.075 404.853]};
624 BadSegments{8} = {...
625 [238.505 238.546; 256.354 257.224; 316.116 316.167; 341.519 341.558; 356.493 356.566; 380.095 380.170; 391.906 392.048; 448.457 448.562; 469.931 470.028; 530.488 530.575; 555.180 558.136; 562.152 562.245; 588.403 588.502; 625.205 625.662; 638.019 638.438; 649.982 650.008; 650.691 651.357; 651.925 652.061; 665.445 665.472; 695.923 696.015; 706.528 706.720; 729.706 732.534], ...
626 [99.546 106.114; 113.245 114.199; 150.885 154.989; 277.486 278.075; 333.645 335.574; 339.358 340.646; 371.860 375.394; 497.459 499.156], ...
627 [49.008 50.205; 231.446 233.406; 329.590 329.659; 355.101 356.019; 360.733 360.973; 372.955 374.891; 389.283 392.068; 453.610 455.431; 464.632 465.265; 489.209 489.996; 514.777 515.295], ...
628 [178.368 179.232; 293.865 294.521; 418.252 418.314; 450.124 450.209; 480.236 480.445; 492.725 493.975; 495.170 497.624; 500.382 500.459; 504.247 504.402; 628.017 628.079; 628.827 628.905; 630.209 630.332], ...
629 [100.616 101.172; 107.691 108.539; 188.814 188.875; 193.119 193.281; 207.964 208.033; 432.254 432.385; 489.834 489.911; 517.960 518.037; 518.955 519.040; 520.938 521.062; 521.945 522.037; 523.959 524.052; 525.942 526.057; 526.945 527.015; 528.958 529.059; 531.138 531.192; 531.979 532.048; 532.951 533.028; 533.962 534.024], ...
630 [135.997 137.232; 383.565 383.657; 418.763 418.955]};
631 BadSegments{9} = {...
632 [215.107 216.187; 262.388 262.388; 287.519 287.635; 289.895 290.135; 311.999 311.999; 350.161 351.179; 526.154 527.033; 564.999 564.999; 584.935 585.059; 587.999 587.999; 601.999 601.999; 603.999 603.999; 608.999 608.999; 612.999 612.999], ...
633 [47.667 47.775; 49.172 54.681; 67.195 70.805; 78.988 80.477; 138.701 138.948; 138.727 138.727; 138.728 138.728; 138.728 138.728; 138.734 138.734; 138.734 138.734; 138.881 138.881; 138.881 138.881; 138.907 138.907; 140.993 141.093; 141.037 141.037; 141.045 141.045; 155.795 155.864; 155.822 155.822; 155.849 155.849; 168.999 168.999; 206.999 206.999; 219.999 219.999; 225.999 225.999; 226.999 226.999; 228.999 228.999; 236.999 236.999; 242.463 242.463; 242.463 242.463; 242.487 242.487; 247.999 247.999; 251.999 251.999; 252.483 252.483; 253.315 254.163; 265.999 265.999; 267.999 267.999; 272.358 272.358; 272.410 272.410; 298.999 298.999; 300.999 300.999; 314.037 314.037; 314.047 314.047; 321.813 321.813; 321.813 321.813; 321.833 321.833; 329.117 329.117; 329.117 329.117; 329.156 329.156; 346.999 346.999; 347.999 347.999; 349.320 349.320; 349.329 349.329; 352.528 355.869; 364.040 364.040; 396.278 397.420; 404.865 404.865; 407.905 407.905; 407.905 407.905; 407.954 407.954; 418.454 418.454; 418.454 418.454; 418.486 418.486; 441.999 441.999; 444.999 444.999; 447.999 447.999; 453.550 453.650; 454.931 455.055; 457.999 457.999; 479.964 480.079; 481.999 481.999; 482.949 483.073; 488.948 489.064; 511.999 511.999; 520.999 520.999; 523.999 523.999; 526.954 527.069; 533.999 533.999; 537.999 537.999], ...
634 [82.889 83.198; 206.143 207.424; 403.873 404.096; 406.790 407.485; 413.936 414.075; 415.912 416.112; 536.621 537.532], ...
635 [182.999 182.999; 182.999 182.999; 183.999 183.999; 195.999 195.999; 208.999 208.999; 209.999 209.999; 278.601 278.955; 413.913 414.067; 415.250 417.792; 419.940 420.087; 420.999 420.999; 512.999 512.999; 514.363 516.254; 521.917 522.134; 522.999 522.999; 523.915 524.101; 533.999 533.999; 538.999 538.999; 539.892 540.062; 543.999 543.999; 548.874 549.089; 549.900 550.062; 552.755 554.075; 585.999 585.999; 587.957 588.073; 588.999 588.999; 594.999 594.999; 603.971 604.056; 604.928 605.097; 615.986 618.495; 623.999 623.999], ...
636 [53.215 54.203; 164.227 168.965; 201.433 202.775; 292.973 295.889; 303.961 304.817; 309.354 311.236; 313.123 313.639; 322.547 323.017; 331.141 334.852; 356.637 356.985; 367.855 368.079; 369.995 373.459; 377.849 378.142; 406.072 407.306; 436.164 436.665; 458.033 458.905; 516.889 518.656; 517.812 518.684], ...
637 [113.945 115.225; 198.570 198.863; 264.162 264.795; 383.705 385.641; 396.477 397.064; 399.706 406.457; 452.261 453.179; 486.338 487.102; 498.869 499.579; 507.968 508.925; 546.266 547.285; 558.825 560.128]};
638 BadSegments{10} = {...
639 [235.104 236.184; 324.272 325.028; 330.799 331.401; 541.062 541.826; 564.747 565.072], ...
640 [100.581 101.229; 285.644 285.644; 285.644 285.644; 297.979 298.033; 298.999 298.999; 300.949 301.026; 301.999 301.999; 303.999 303.999; 304.999 304.999; 306.999 306.999; 307.999 307.999; 310.999 310.999; 311.999 311.999; 313.971 314.025; 314.999 314.999; 316.995 317.035; 317.999 317.999; 319.999 319.999; 320.923 321.046; 326.971 327.048; 327.999 327.999; 329.999 329.999; 330.999 330.999; 332.974 333.028; 333.999 333.999; 335.971 336.025; 336.999 336.999; 338.973 339.035; 339.999 339.999; 341.951 342.044; 343.999 343.999; 344.964 345.033; 346.999 346.999; 347.999 347.999; 452.015 453.411; 458.735 459.776; 467.974 468.089], ...
641 [41.266 41.675; 53.905 55.240; 159.159 159.345; 220.255 220.394], ...
642 [66.751 67.190; 201.674 201.812; 294.119 295.168; 303.188 303.528; 316.992 317.037; 317.999 317.999; 317.999 317.999; 319.999 319.999; 320.980 321.042; 322.999 322.999; 325.999 325.999; 326.955 327.048; 328.999 328.999; 333.999 333.999; 334.999 334.999; 342.999 342.999; 343.999 343.999; 351.915 352.038; 352.999 352.999; 407.979 408.056; 409.999 409.999; 411.999 411.999; 415.405 416.154; 435.999 435.999; 436.962 437.046; 468.885 469.100; 469.999 469.999; 470.999 470.999; 516.210 516.357], ...
643 [105.369 106.172; 141.468 142.178; 199.008 199.818; 201.269 201.716; 352.851 353.083; 449.865 452.041; 459.508 459.802], ...
644 [229.948 230.033; 230.999 230.999; 230.999 230.999; 259.588 259.990; 343.970 345.798; 361.999 361.999; 362.970 363.046; 364.999 364.999; 366.999 366.999; 367.962 368.031; 372.521 374.179; 405.999 405.999; 409.999 409.999; 411.999 411.999; 412.999 412.999; 434.999 434.999; 435.970 436.031; 516.999 516.999; 519.999 519.999]};
645 BadSegments{11} = {...
646 [179.045 180.225; 323.999 323.999; 323.999 323.999; 324.999 324.999; 327.978 328.025; 328.966 329.028; 330.999 330.999; 365.999 365.999; 367.999 367.999; 370.999 370.999; 371.999 371.999; 373.999 373.999; 375.965 376.042; 377.999 377.999], ...
647 [52.107 53.156; 521.077 521.155], ...
648 [65.331 66.156], ...
649 [81.579 82.143; 108.565 108.565; 108.566 108.566; 112.176 112.176; 122.377 122.377; 122.565 122.565; 213.882 213.882; 215.305 215.305; 224.851 224.851; 224.919 224.919; 255.815 255.815; 257.893 257.893; 359.952 359.952; 361.630 361.754; 370.285 370.285; 376.853 376.853; 511.600 511.600; 513.631 513.631; 513.988 513.988; 518.215 518.215], ...
650 [63.205 64.154; 170.951 171.036; 176.841 176.841; 176.842 176.842; 177.282 177.282; 223.886 223.971; 259.963 259.963; 261.547 261.547; 341.185 341.302; 368.999 368.999; 370.999 370.999; 374.999 374.999; 382.971 383.033; 383.999 383.999; 386.999 386.999; 388.958 389.035; 390.999 390.999; 391.955 392.031; 394.955 395.040; 396.999 396.999; 398.999 398.999; 400.999 400.999; 402.999 402.999; 404.963 405.033; 406.999 406.999; 429.829 429.829; 430.346 430.346; 465.184 465.184; 470.290 470.290], ...
651 [50.195 51.145; 158.850 159.012]};
652 BadSegments{12} = {...
653 [193.435 194.175; 500.000 501.000; 08.988 509.868; 528.999 528.999; 528.999 528.999; 529.999 529.999; 531.999 531.999; 547.999 547.999], ...
654 [133.484 134.185; 134.911 135.065; 553.999 553.999; 553.999 553.999; 554.999 554.999; 557.999 557.999; 558.999 558.999; 564.999 564.999; 565.977 566.046; 568.999 568.999; 569.951 570.028; 571.999 571.999; 579.959 580.028; 580.977 581.055; 583.971 584.033; 583.999 583.999; 585.999 585.999; 586.999 586.999; 588.980 589.026; 590.999 590.999; 591.958 592.044; 595.999 595.999], ...
655 [46.028 47.216; 129.557 130.236; 200.999 200.999; 200.999 200.999; 201.975 202.075; 203.999 203.999; 204.967 205.053; 213.627 214.515; 218.958 219.044; 222.959 228.252; 309.999 309.999; 311.897 317.537; 311.999 311.999; 351.968 353.234; 399.999 399.999; 446.508 451.454; 487.999 487.999; 512.278 512.926], ...
656 [82.535 84.062; 102.247 102.355; 134.999 134.999; 134.999 134.999; 136.999 136.999; 138.973 139.042; 147.999 147.999; 148.999 148.999; 149.999 149.999; 193.999 193.999; 194.999 194.999; 224.984 226.095; 241.954 242.077; 243.948 244.087; 280.999 280.999; 281.999 281.999; 305.000 305.451; 310.945 311.068; 328.999 328.999; 352.999 352.999; 353.999 353.999; 397.025 397.411; 415.944 418.096; 415.999 415.999; 470.999 470.999; 477.971 478.041; 483.997 484.737; 492.958 493.089; 493.999 493.999; 494.999 494.999; 522.999 522.999; 523.999 523.999; 524.955 525.039], ...
657 [175.183 176.155; 246.112 246.991; 412.005 413.340; 483.915 484.061; 485.959 486.028; 497.360 498.880; 594.457 594.944; 596.641 598.006; 615.277 618.710], ...
658 [66.900 72.232; 75.510 78.688; 543.495 545.999]};
659 BadSegments{13} = {...
660 [307.246 308.179; 627.881 628.089; 629.941 630.049], ...
661 [171.506 172.301; 172.999 172.999; 430.999 430.999; 432.999 432.999; 434.999 434.999; 448.999 448.999; 479.999 479.999; 489.999 489.999; 490.999 490.999; 491.999 491.999], ...
662 [92.059 93.209], ...
663 [52.791 53.231; 54.999 54.999; 65.985 68.138; 91.240 91.386; 92.137 92.207; 105.346 105.493; 121.120 121.398; 146.546 146.955; 194.025 197.652; 242.985 243.571; 247.101 247.556; 269.889 270.083; 270.946 271.070; 274.408 275.866; 294.565 295.267; 319.370 319.879; 365.999 365.999; 375.913 376.044; 376.869 377.055; 377.999 377.999; 390.130 393.225; 403.965 404.035; 404.953 405.075; 419.265 419.565; 427.015 427.154; 427.879 428.118; 427.999 427.999; 428.913 429.067; 480.945 482.095; 484.285 484.571; 516.929 517.099; 517.963 518.079], ...
664 [115.921 116.060; 117.999 117.999; 120.999 120.999; 126.896 127.058; 130.955 131.039; 131.957 132.043; 132.961 133.015; 134.999 134.999; 135.950 136.043; 139.999 139.999; 143.999 143.999; 144.850 145.066; 145.999 145.999; 146.999 146.999; 160.929 161.045; 161.999 161.999; 189.086 189.310; 193.939 194.063; 195.975 196.045; 199.961 200.045; 201.952 202.059; 202.939 205.084; 210.999 210.999; 211.738 213.629; 217.954 218.061; 218.987 219.049; 219.975 220.028; 258.953 259.037; 259.952 260.045; 260.963 261.032; 261.958 262.043; 262.954 263.054; 262.999 262.999; 288.999 288.999; 295.477 295.655; 298.976 299.054; 299.979 300.018; 300.975 301.005; 336.952 337.044; 337.977 338.032; 338.988 339.027; 338.999 338.999; 339.991 340.045; 340.975 341.029; 341.978 342.016; 343.976 344.054; 361.961 362.045; 365.942 366.050; 370.999 370.999; 384.961 385.045; 409.977 410.047; 415.984 416.030; 426.944 427.059; 430.999 430.999; 436.999 436.999; 448.999 448.999; 449.500 452.131; 481.962 482.055; 482.973 483.027; 484.975 485.060; 503.999 503.999; 504.999 504.999; 507.967 508.028; 508.955 509.032; 510.999 510.999; 512.999 512.999; 518.865 520.292; 522.958 523.043; 523.999 523.999; 524.948 525.034; 525.959 526.044; 526.946 527.055; 527.942 528.027; 528.961 529.053; 529.945 530.022; 535.999 535.999; 536.957 537.058; 538.967 539.036; 539.963 540.040; 541.976 542.045; 543.999 543.999; 551.956 552.034; 552.990 553.028; 553.977 554.024; 555.968 556.022; 556.204 557.454; 557.963 558.032; 559.969 560.023; 563.973 564.035; 563.999 563.999], ...
665 [87.308 87.639; 107.039 108.189; 427.943 428.035; 437.965 438.027; 439.973 440.026; 491.275 492.571]};
666 BadSegments{14} = {...
667 [365.982 367.194; 368.999 368.999; 368.999 368.999; 369.999 369.999; 371.999 371.999; 373.999 373.999; 375.942 376.050; 376.999 376.999; 378.999 378.999; 380.999 380.999; 382.999 382.999; 383.999 383.999; 386.999 386.999; 387.999 387.999; 418.999 418.999; 444.999 444.999; 690.178 693.218], ...
668 [101.796 102.183; 218.999 218.999; 219.999 219.999; 221.999 221.999; 222.999 222.999; 227.999 227.999; 229.999 229.999; 230.999 230.999; 232.999 232.999; 233.999 233.999; 235.999 235.999; 237.999 237.999; 238.985 239.031; 240.999 240.999; 242.999 242.999; 243.999 243.999; 246.999 246.999; 247.999 247.999; 253.999 253.999; 258.999 258.999; 259.999 259.999; 260.227 261.123; 264.999 264.999; 265.999 265.999; 268.999 268.999; 269.999 269.999; 274.999 274.999; 276.999 276.999; 277.999 277.999; 280.999 280.999; 282.966 283.021; 284.999 284.999; 285.999 285.999; 360.999 360.999; 362.973 363.026; 364.999 364.999; 365.999 365.999; 367.999 367.999; 368.985 369.024; 370.999 370.999; 371.999 371.999; 378.999 378.999; 379.999 379.999; 381.999 381.999; 383.999 383.999; 385.999 385.999; 387.999 387.999; 388.999 388.999; 398.999 398.999; 415.999 415.999; 417.999 417.999; 418.999 418.999; 421.999 421.999; 422.999 422.999], ...
669 [89.285 90.187], ...
670 [85.991 87.179; 88.999 88.999; 89.999 89.999; 92.966 93.027; 93.999 93.999; 107.999 107.999; 110.999 110.999; 111.971 112.025; 118.999 118.999; 121.999 121.999; 122.999 122.999; 166.999 166.999; 168.957 169.035; 173.999 173.999; 174.999 174.999; 175.957 176.035; 198.999 198.999; 199.999 199.999; 202.999 202.999; 203.999 203.999; 205.999 205.999; 207.999 207.999; 208.999 208.999; 210.974 211.044; 211.999 211.999; 212.999 212.999; 232.984 233.023; 234.999 234.999; 235.999 235.999; 236.999 236.999; 239.958 240.044; 240.999 240.999], ...
671 [71.132 72.227], ...
672 [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]};
673 BadSegments{15} = {...
674 [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], ...
675 [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], ...
676 [53.557 54.175; 148.851 149.136], ...
677 [43.681 44.214; 361.255 361.587; 409.462 411.021], ...
678 [90.868 91.130; 410.935 411.044], ...
679 [64.786 65.141; 132.385 132.786; 177.735 178.252; 278.747 278.902; 313.959 314.028; 314.970 315.031]};
680 BadSegments{16} = {...
681 [38.958 44.335; 305.280 312.826; 324.778 326.067; 393.183 398.367; 403.410 422.854], ...
682 [49.726 50.251; 58.675 65.465; 263.918 264.088; 321.795 322.195; 522.881 523.081], ...
683 [61.245 62.325; 65.628 65.905; 315.686 317.275; 335.184 336.449; 387.870 388.117; 389.892 390.062], ...
684 [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], ...
685 [71.665 72.513; 76.347 77.181; 127.134 128.862], ...
686 [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]};
687 BadSeg = BadSegments{iSubj}{iRun}';
688 end
689
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.
External Matlab call
To call a Brainstorm script directly from the command line of a terminal and avoid the graphical environment of Matlab to get started, on Linux or MacOS, you can use the syntax:
matlab -nosplash -nodesktop -r "run('/path/to/script.m');"
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.
Send report by email
When running some long computation on a distant server, it can be convenient to receive an email when the processing is over. Two solutions for sending yourself an email from Brainstorm: from the pipeline editor, or directly from a script.
Use the process File > Send report by email to send the current execution report:
Brainstorm username: The user name you use to download Brainstorm from the website, or to post messages on the user forum. The email associated with this account is the primary recipient of the email.
Send copy to: Optional, sends a copy to an additional email address. Use this to notify collaborator, or receive the notification on an email address that is not registered on the Brainstorm website.
Subject: Subject of the email.
Send full report: If selected, sends the full HTML execution report as displayed by the Report viewer. Be careful when working with sensitive patient data, as it would send with no encryption the full file names of all the files. If not selected, only the name of the processes and execution times are sent, in plain text.
Alternatively, use one of the following options (isFullReport can be set to 0 or 1):
% At the end of your script
ReportFile = bst_report('Save', sFiles);
bst_report('Email', ReportFile, username, to, subject, isFullReport);
% Anywhere in your script
bst_report('Email', 'current', username, to, subject, isFullReport);
How to compile Brainstorm
Brainstorm can be compiled as a JAR application using the function bst_compile.m. You would need this in order to execute without Matlab a modified version of Brainstorm.
Software requirements:
MATLAB >= 2020a
- MATLAB Compiler toolbox
- MATLAB Compiler SDK toolbox
Open JDK 8: https://adoptopenjdk.net/?variant=openjdk8
Set the environment variable JAVA_HOME to the installation folder of the JDK.
Windows 10: Right-click on "This PC" > Advanced system settings > Environment variables
To compile Brainstorm, run from the command line:
brainstorm compile: Compiles Brainstorm together with manyplugins: SPM12, FieldTrip, Brain2mesh, Iso2mesh, BrainEntropy, LibSVM, NIRSTORM. At the moment, this works only from a Windows 10 computer (but will be extended later to other OS).
brainstorm compile noplugs: Compile Brainstorm without the extra plugins. This should work on all the operating systems.
Additional documentation
Tutorial: How to write your own process
Tutorial: Java in Brainstorm
Forum: Memory management
Forum: How to compile Brainstorm (outdated, see compilation section above instead)