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| ''Authors: Francois Tadel'' |
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| Select the menu File > Create new protocol. Name it "'''!TutorialScript'''" and select the options: | Select the menu File > Create new protocol. Name it "'''TutorialScript'''" and select the options: |
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| To start building your analysis pipeline, just click on the "'''Run'''" button in the Process1 tab. Then add all the processes listed below. The output of each process is the input of the following one, this is why they cannot necessarily be shuffled. === Import anatomy > Import FreeSurfer folder === * Subject name: Subject01 * Folder to import: Select the folder sample_raw/Anatomy * Number of vertices (cortex): 15000 |
To start building your analysis pipeline, just click on the "'''Run'''" button in the Process1 tab. We don't need any file in input, as we are going to select the files to import in the script itself. Then add all the processes listed below. The output of each process is the input of the following one, this is why the order of the processes is important. === Import anatomy > Import anatomy folder === * Folder to import: sample_raw/Anatomy <<BR>>File format: "FreeSurfer folder" |
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| {{attachment:procImportFs.gif}} === Import recordings > Create link to raw file === Input: None; Output: Raw file {{attachment:procLinkRaw.gif|procImportFs.gif}} === Pre-process > Sinusoid removal (notch) === |
{{attachment:process_import_freesurfer.gif}} === Import -> Import recordings > Create link to raw file === * File to import: Select the folder sample_raw/Data/subj001_somatosensory_20111109_01_AUX-f.ds * Input: None; Output: Raw file {{attachment:process_import_data_raw.gif}} === Pre-process > Notch filter === |
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| {{attachment:procSin.gif|procImportFs.gif}} === Artifacts > Detect eye blinks === |
{{attachment:process_sin_remove.gif}} === Events > Detect eye blinks === |
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| {{attachment:procDetectEog.gif|procImportFs.gif}} === Artifacts > Compute SSP: eye blinks === |
{{attachment:process_evt_detect_eog.gif}} === Events > Compute SSP: eye blinks === |
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| {{attachment:procSspEog.gif|procImportFs.gif}} === Import recordings > Import MEG/EEG : Events === |
{{attachment:process_ssp_eog.gif}} === Import -> Import recordings > Import MEG/EEG : Events === |
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| {{attachment:procImportEvt.gif|procImportFs.gif}} | {{attachment:process_import_data_event.gif}} |
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| {{attachment:procBaseline.gif|procImportFs.gif}} | {{attachment:process_baseline.gif}} === Pre-process > Add time offset === Input: 199 epochs ; Output: 199 epochs {{attachment:process_timeoffset.gif}} |
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| {{attachment:procNoiseCov.gif|procImportFs.gif}} | {{attachment:process_noisecov.gif}} |
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| {{attachment:procAverage.gif|procImportFs.gif}} | {{attachment:process_average.gif}} |
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| {{attachment:procSnapReg.gif|procImportFs.gif}} | {{attachment:process_snapshot.gif}} |
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| {{attachment:procSnapTs.gif|procImportFs.gif}} | {{attachment:process_snapshot2.gif}} |
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| {{attachment:procHeadmodel.gif|procImportFs.gif}} | {{attachment:process_headmodel.gif}} |
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| {{attachment:procSources.gif|procImportFs.gif}} | {{attachment:process_inverse.gif}} |
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| Use the menus on top of the pipeline editor to save this list of processes on your computer. The menu "Save > New..." will create an entry readily available in your Brainstorm installation. {{attachment:savePipeline.gif|procImportFs.gif}} |
Use the menus on top of the pipeline editor to save this list of processes on your computer. The menu "Save > New..." will create an entry readily available in your Brainstorm installation in the Load section of the same menu. {{attachment:savePipeline.gif}} |
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| This script is also available in the Brainstorm distribution: '''brainstorm3/toolbox/script/tutorial_raw.m ''' |
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| % Script generated by Brainstorm v3.1 (11-Jan-2013) | % Script generated by Brainstorm v3.2 (22-Jul-2014) |
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| FileNamesA = []; | sFiles = []; SubjectNames = {... 'Subject01'}; RawFiles = {... 'C:\Work\RawData\Tutorials\sample_raw\Anatomy', ... 'C:\Work\RawData\Tutorials\sample_raw\Data\subj001_somatosensory_20111109_01_AUX-f.ds'}; |
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| bst_report('Start', FileNamesA); % Process: Import FreeSurfer folder sFiles = bst_process(... 'CallProcess', 'process_import_freesurfer', ... FileNamesA, [], ... 'subjectname', 'Subject01', ... 'mrifile', {'C:\Work\RawData\Tutorials\sample_raw\Anatomy', 'FsDir', [...] |
bst_report('Start', sFiles); % Process: Import anatomy folder sFiles = bst_process('CallProcess', 'process_import_anatomy', ... sFiles, [], ... 'subjectname', SubjectNames{1}, ... 'mrifile', {RawFiles{1}, 'FreeSurfer'}, ... |
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| 'nas', [126, 215, 138], ... 'lpa', [58, 136, 121], ... 'rpa', [197, 138, 118], ... 'ac', [128, 137, 157], ... 'pc', [128, 113, 157], ... 'ih', [128, 125, 216]); |
'nas', [127, 212, 123], ... 'lpa', [55, 124, 119], ... 'rpa', [200, 129, 114], ... 'ac', [129, 137, 157], ... 'pc', [129, 113, 157], ... 'ih', [129, 118, 209]); |
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| sFiles = bst_process(... 'CallProcess', 'process_import_data_raw', ... sFiles, [], ... 'subjectname', 'Subject01', ... 'datafile', {'C:\Work\RawData\Tutorials\sample_raw\Data\EF1982_somatosensory_ [...] |
sFiles = bst_process('CallProcess', 'process_import_data_raw', ... sFiles, [], ... 'subjectname', SubjectNames{1}, ... 'datafile', {RawFiles{2}, 'CTF'}, ... 'channelreplace', 1, ... |
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| % Process: Sinusoid removal: 60Hz 120Hz 180Hz sFiles = bst_process(... 'CallProcess', 'process_sin_remove', ... |
% Process: Notch filter: 60Hz 120Hz 180Hz sFiles = bst_process('CallProcess', 'process_notch', ... |
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| 'reverse', 1); | 'read_all', 0); |
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| sFiles = bst_process(... 'CallProcess', 'process_evt_detect_eog', ... |
sFiles = bst_process('CallProcess', 'process_evt_detect_eog', ... |
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| 'timewindow', [0, 359.999167], ... | 'timewindow', [], ... |
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| % Process: Detect heartbeats sFiles = bst_process('CallProcess', 'process_evt_detect_ecg', ... sFiles, [], ... 'channelname', 'EEG057', ... 'timewindow', [], ... 'eventname', 'cardiac'); |
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| sFiles = bst_process(... 'CallProcess', 'process_ssp_eog', ... |
sFiles = bst_process('CallProcess', 'process_ssp_eog', ... |
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| 'sensortypes', 'MEG, MEG MAG, MEG GRAD'); | 'sensortypes', 'MEG, EEG', ... 'usessp', 0); |
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| sFiles = bst_process(... 'CallProcess', 'process_import_data_event', ... sFiles, [], ... 'subjectname', 'Subject01', ... |
sFiles = bst_process('CallProcess', 'process_import_data_event', ... sFiles, [], ... 'subjectname', SubjectNames{1}, ... |
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| 'timewindow', [0, 359.999167], ... 'epochtime', {[-100, 300], 'ms'}, ... |
'timewindow', [], ... 'epochtime', [-0.1, 0.3], ... |
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| 'baseline', []); % Process: Remove baseline: [-100ms,0ms] sFiles = bst_process(... 'CallProcess', 'process_baseline', ... sFiles, [], ... 'baseline', [-0.10001, -0.00017], ... 'sensortypes', 'MEG, EEG', ... |
'baseline', [-0.1, -0.0008333333333]); % Process: Add time offset: -4.20ms sFiles = bst_process('CallProcess', 'process_timeoffset', ... sFiles, [], ... 'offset', -0.0042, ... |
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| sFiles = bst_process(... 'CallProcess', 'process_noisecov', ... sFiles, [], ... 'baseline', [-0.10001, -0.000843], ... |
sFiles = bst_process('CallProcess', 'process_noisecov', ... sFiles, [], ... 'baseline', [-0.1042, 0], ... |
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| 'method', 1, ... | 'method', 1, ... % Full noise covariance matrix |
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| % Process: Average: By condition sFiles = bst_process(... 'CallProcess', 'process_average', ... sFiles, [], ... 'avgtype', 3); |
% Process: Average: By condition (subject average) sFiles = bst_process('CallProcess', 'process_average', ... sFiles, [], ... 'avgtype', 3, ... 'avg_func', 1, ... % Arithmetic average: mean(x) 'keepevents', 0); |
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| sFiles = bst_process(... 'CallProcess', 'process_snapshot', ... sFiles, [], ... 'target', {1, {'Sensors/MRI registration', [...] 'modality', {1, {'MEG (All)', 'MEG (Gradiometers)', 'MEG (Magnetometers)', 'EEG'}}, ... 'orient', {1, {'left', 'right', 'top', 'bottom', 'front', 'back'}}, ... |
sFiles = bst_process('CallProcess', 'process_snapshot', ... sFiles, [], ... 'target', 1, ... % Sensors/MRI registration 'modality', 1, ... % MEG (All) 'orient', 1, ... % left |
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| 'contact', '0.000, 0.100, 12', ... 'comment', 'Registration'); |
'contact_time', [0, 0.1], ... 'contact_nimage', 12, ... 'comment', 'MEG/MRI Registration'); |
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| sFiles = bst_process(... 'CallProcess', 'process_snapshot', ... sFiles, [], ... 'target', {5, {'Sensors/MRI registration', [...] 'modality', {1, {'MEG (All)', 'MEG (Gradiometers)', 'MEG (Magnetometers)', 'EEG'}}, ... 'orient', {1, {'left', 'right', 'top', 'bottom', 'front', 'back'}}, ... |
sFiles = bst_process('CallProcess', 'process_snapshot', ... sFiles, [], ... 'target', 5, ... % Recordings time series 'modality', 1, ... % MEG (All) 'orient', 1, ... % left |
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| 'contact', '0.000, 0.100, 12', ... 'comment', 'Evoked responses'); % Process: Snapshot: Recordings topography (one time) sFiles = bst_process(... 'CallProcess', 'process_snapshot', ... sFiles, [], ... 'target', {6, {'Sensors/MRI registration', [...] 'modality', {1, {'MEG (All)', 'MEG (Gradiometers)', 'MEG (Magnetometers)', 'EEG'}}, ... 'orient', {1, {'left', 'right', 'top', 'bottom', 'front', 'back'}}, ... 'time', 0.035, ... 'contact', '0.000, 0.100, 12', ... 'comment', 'Evoked responses'); |
'contact_time', [0, 0.1], ... 'contact_nimage', 12, ... 'comment', 'Evoked response'); |
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| sFiles = bst_process(... 'CallProcess', 'process_headmodel', ... sFiles, [], ... |
sFiles = bst_process('CallProcess', 'process_headmodel', ... sFiles, [], ... 'comment', '', ... |
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| 'meg', {3, {'<none>', 'Single sphere', 'Overlapping spheres', 'OpenMEEG BEM'}}, ... 'eeg', {3, {'<none>', '3-shell sphere', 'OpenMEEG BEM'}}, ... |
'meg', 3, ... % Overlapping spheres 'eeg', 3, ... % OpenMEEG BEM 'ecog', 2, ... % OpenMEEG BEM 'seeg', 2, ... |
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| sFiles = bst_process(... 'CallProcess', 'process_inverse', ... sFiles, [], ... 'method', 1, ... |
sFiles = bst_process('CallProcess', 'process_inverse', ... sFiles, [], ... 'comment', '', ... 'method', 1, ... % Minimum norm estimates (wMNE) |
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| 'ChannelTypes', {{}}, ... | |
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| 'ecogreg', 0.1, ... 'seegreg', 0.1, ... |
|
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| 'output', 1); | 'output', 1); % Kernel only: shared |
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| == Process report == Click on Run to start the pipeline. As this process is taking screen captures, do not use your computer for something else at the same time: if another window covers the Brainstorm figure, it will not capture the right image. |
== Report viewer == Click on Run to start the script. As this process is taking screen captures, do not use your computer for something else at the same time: if another window covers the Brainstorm figures, it will not capture the right images. At the end, the report viewer is opened to show the status of all the processes, the information messages, the list of input and output files, and the screen captures. The report is saved in your home folder ($home/.brainstorm/reports). If you close this window, you can get it back with the menu File > Report viewer. {{attachment:report1.gif}} {{attachment:report2.gif}} <<EmbedContent(http://neuroimage.usc.edu/bst/get_feedback.php?Tutorials/TutRawScript)>> |
Full analysis with one script
Authors: Francois Tadel
This tutorial explains how to use the Brainstorm scripting interface to run a full analysis, from the raw recordings to the source reconstruction. It is based on a median nerve stimulation experiment recorded at the Montreal Neurological Institute in 2011 with a CTF MEG 275 system. The sample dataset contains 6 minutes of recordings at 1200Hz for one subject and includes 100 stimulations of each arm.
The tutorial follows the analysis steps detailed in the three advanced tutorials in the category Processing continuous recordings. You should read them before reading this tutorial, to have the explanations that go with the analysis steps.
Contents
-
Creating the analysis pipeline
- Import anatomy > Import anatomy folder
- Import -> Import recordings > Create link to raw file
- Pre-process > Notch filter
- Events > Detect eye blinks
- Events > Compute SSP: eye blinks
- Import -> Import recordings > Import MEG/EEG : Events
- Pre-process > Remove DC offset
- Pre-process > Add time offset
- Sources > Compute noise covariance
- Average > Average files
- File > Save snapshot: Sensors/MRI registration
- File > Save snapshot: Recordings time series
- Sources > Compute head model
- Sources > Compute sources
- Save the pipeline
- Report viewer
Creating the analysis pipeline
Select the menu File > Create new protocol. Name it "TutorialScript" and select the options:
"No, use individual anatomy",
"Yes, use one channel file per subject".
To start building your analysis pipeline, just click on the "Run" button in the Process1 tab. We don't need any file in input, as we are going to select the files to import in the script itself. Then add all the processes listed below. The output of each process is the input of the following one, this is why the order of the processes is important.
Import anatomy > Import anatomy folder
Folder to import: sample_raw/Anatomy
File format: "FreeSurfer folder"- Fiducials: Copy what is indicated below. This is a reason it is usually easier to do this step in interactive mode, and then run only the script starting from the next step.
- Input: None; Output: None
Import -> Import recordings > Create link to raw file
- File to import: Select the folder sample_raw/Data/subj001_somatosensory_20111109_01_AUX-f.ds
- Input: None; Output: Raw file
Pre-process > Notch filter
Input: Raw file ; Output: Raw file (new)
Events > Detect eye blinks
Input: Raw file ; Output: Raw file
Events > Compute SSP: eye blinks
Input: Raw file ; Output: Raw file
Import -> Import recordings > Import MEG/EEG : Events
Input: Raw file ; Output: 199 epochs in 2 conditions
Pre-process > Remove DC offset
Input: 199 epochs ; Output: 199 epochs
Pre-process > Add time offset
Input: 199 epochs ; Output: 199 epochs
Sources > Compute noise covariance
Since the epochs are currently selected and pre-processed: we can use them to estimate the noise covariance matrix before we move on with the calculation of the average.
Input: 199 epochs ; Output: 199 epochs
Average > Average files
Input: 199 epochs ; Output: 2 averages
File > Save snapshot: Sensors/MRI registration
Input: 2 averages ; Output: 2 averages
File > Save snapshot: Recordings time series
Input: 2 averages ; Output: 2 averages
Sources > Compute head model
Input: 2 averages ; Output: 2 averages
Sources > Compute sources
Input: 2 averages ; Output: all the source files (1 raw + 2 average + 199 epochs = 202 files)
Save the pipeline
Save in current workspace
Use the menus on top of the pipeline editor to save this list of processes on your computer. The menu "Save > New..." will create an entry readily available in your Brainstorm installation in the Load section of the same menu.
Export as script
Use the menu "Generate .m script" to create a Matlab script that would have the exact same result as running this analysis pipeline from the Brainstorm interface.
This script is also available in the Brainstorm distribution: brainstorm3/toolbox/script/tutorial_raw.m
% Script generated by Brainstorm v3.2 (22-Jul-2014)
% Input files
sFiles = [];
SubjectNames = {...
'Subject01'};
RawFiles = {...
'C:\Work\RawData\Tutorials\sample_raw\Anatomy', ...
'C:\Work\RawData\Tutorials\sample_raw\Data\subj001_somatosensory_20111109_01_AUX-f.ds'};
% Start a new report
bst_report('Start', sFiles);
% Process: Import anatomy folder
sFiles = bst_process('CallProcess', 'process_import_anatomy', ...
sFiles, [], ...
'subjectname', SubjectNames{1}, ...
'mrifile', {RawFiles{1}, 'FreeSurfer'}, ...
'nvertices', 15000, ...
'nas', [127, 212, 123], ...
'lpa', [55, 124, 119], ...
'rpa', [200, 129, 114], ...
'ac', [129, 137, 157], ...
'pc', [129, 113, 157], ...
'ih', [129, 118, 209]);
% Process: Create link to raw file
sFiles = bst_process('CallProcess', 'process_import_data_raw', ...
sFiles, [], ...
'subjectname', SubjectNames{1}, ...
'datafile', {RawFiles{2}, 'CTF'}, ...
'channelreplace', 1, ...
'channelalign', 1);
% Process: Notch filter: 60Hz 120Hz 180Hz
sFiles = bst_process('CallProcess', 'process_notch', ...
sFiles, [], ...
'freqlist', [60, 120, 180], ...
'sensortypes', 'MEG, EEG', ...
'read_all', 0);
% Process: Detect eye blinks
sFiles = bst_process('CallProcess', 'process_evt_detect_eog', ...
sFiles, [], ...
'channelname', 'EEG058', ...
'timewindow', [], ...
'eventname', 'blink');
% Process: Detect heartbeats
sFiles = bst_process('CallProcess', 'process_evt_detect_ecg', ...
sFiles, [], ...
'channelname', 'EEG057', ...
'timewindow', [], ...
'eventname', 'cardiac');
% Process: SSP EOG: blink
sFiles = bst_process('CallProcess', 'process_ssp_eog', ...
sFiles, [], ...
'eventname', 'blink', ...
'sensortypes', 'MEG, EEG', ...
'usessp', 0);
% Process: Import MEG/EEG: Events
sFiles = bst_process('CallProcess', 'process_import_data_event', ...
sFiles, [], ...
'subjectname', SubjectNames{1}, ...
'condition', '', ...
'eventname', 'left, right', ...
'timewindow', [], ...
'epochtime', [-0.1, 0.3], ...
'createcond', 1, ...
'ignoreshort', 1, ...
'usectfcomp', 1, ...
'usessp', 1, ...
'freq', [], ...
'baseline', [-0.1, -0.0008333333333]);
% Process: Add time offset: -4.20ms
sFiles = bst_process('CallProcess', 'process_timeoffset', ...
sFiles, [], ...
'offset', -0.0042, ...
'overwrite', 1);
% Process: Compute noise covariance
sFiles = bst_process('CallProcess', 'process_noisecov', ...
sFiles, [], ...
'baseline', [-0.1042, 0], ...
'dcoffset', 1, ...
'method', 1, ... % Full noise covariance matrix
'copycond', 0, ...
'copysubj', 0);
% Process: Average: By condition (subject average)
sFiles = bst_process('CallProcess', 'process_average', ...
sFiles, [], ...
'avgtype', 3, ...
'avg_func', 1, ... % Arithmetic average: mean(x)
'keepevents', 0);
% Process: Snapshot: Sensors/MRI registration
sFiles = bst_process('CallProcess', 'process_snapshot', ...
sFiles, [], ...
'target', 1, ... % Sensors/MRI registration
'modality', 1, ... % MEG (All)
'orient', 1, ... % left
'time', 0, ...
'contact_time', [0, 0.1], ...
'contact_nimage', 12, ...
'comment', 'MEG/MRI Registration');
% Process: Snapshot: Recordings time series
sFiles = bst_process('CallProcess', 'process_snapshot', ...
sFiles, [], ...
'target', 5, ... % Recordings time series
'modality', 1, ... % MEG (All)
'orient', 1, ... % left
'time', 0, ...
'contact_time', [0, 0.1], ...
'contact_nimage', 12, ...
'comment', 'Evoked response');
% Process: Compute head model
sFiles = bst_process('CallProcess', 'process_headmodel', ...
sFiles, [], ...
'comment', '', ...
'sourcespace', 1, ...
'meg', 3, ... % Overlapping spheres
'eeg', 3, ... % OpenMEEG BEM
'ecog', 2, ... % OpenMEEG BEM
'seeg', 2, ...
'openmeeg', struct(...
'BemFiles', {{}}, ...
'BemNames', {{'Scalp', 'Skull', 'Brain'}}, ...
'BemCond', [1, 0.0125, 1], ...
'BemSelect', [1, 1, 1], ...
'isAdjoint', 0, ...
'isAdaptative', 1, ...
'isSplit', 0, ...
'SplitLength', 4000));
% Process: Compute sources
sFiles = bst_process('CallProcess', 'process_inverse', ...
sFiles, [], ...
'comment', '', ...
'method', 1, ... % Minimum norm estimates (wMNE)
'wmne', struct(...
'NoiseCov', [], ...
'InverseMethod', 'wmne', ...
'ChannelTypes', {{}}, ...
'SNR', 3, ...
'diagnoise', 0, ...
'SourceOrient', {{'fixed'}}, ...
'loose', 0.2, ...
'depth', 1, ...
'weightexp', 0.5, ...
'weightlimit', 10, ...
'regnoise', 1, ...
'magreg', 0.1, ...
'gradreg', 0.1, ...
'eegreg', 0.1, ...
'ecogreg', 0.1, ...
'seegreg', 0.1, ...
'fMRI', [], ...
'fMRIthresh', [], ...
'fMRIoff', 0.1, ...
'pca', 1), ...
'sensortypes', 'MEG, MEG MAG, MEG GRAD, EEG', ...
'output', 1); % Kernel only: shared
% Save and display report
ReportFile = bst_report('Save', sFiles);
bst_report('Open', ReportFile);
Report viewer
Click on Run to start the script.
As this process is taking screen captures, do not use your computer for something else at the same time: if another window covers the Brainstorm figures, it will not capture the right images.
At the end, the report viewer is opened to show the status of all the processes, the information messages, the list of input and output files, and the screen captures. The report is saved in your home folder ($home/.brainstorm/reports). If you close this window, you can get it back with the menu File > Report viewer.
