9963
Comment:
|
9786
|
Deletions are marked like this. | Additions are marked like this. |
Line 14: | Line 14: |
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. | 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. |
Line 28: | Line 28: |
{{attachment:procLinkRaw.gif|procImportFs.gif}} | {{attachment:procLinkRaw.gif}} |
Line 33: | Line 33: |
{{attachment:procSin.gif|procImportFs.gif}} | {{attachment:procSin.gif}} |
Line 38: | Line 38: |
{{attachment:procDetectEog.gif|procImportFs.gif}} | {{attachment:procDetectEog.gif}} |
Line 43: | Line 43: |
{{attachment:procSspEog.gif|procImportFs.gif}} | {{attachment:procSspEog.gif}} |
Line 48: | Line 48: |
{{attachment:procImportEvt.gif|procImportFs.gif}} | {{attachment:procImportEvt.gif}} |
Line 53: | Line 53: |
{{attachment:procBaseline.gif|procImportFs.gif}} | {{attachment:procBaseline.gif}} |
Line 60: | Line 60: |
{{attachment:procNoiseCov.gif|procImportFs.gif}} | {{attachment:procNoiseCov.gif}} |
Line 65: | Line 65: |
{{attachment:procAverage.gif|procImportFs.gif}} | {{attachment:procAverage.gif}} |
Line 70: | Line 70: |
{{attachment:procSnapReg.gif|procImportFs.gif}} | {{attachment:procSnapReg.gif}} |
Line 75: | Line 75: |
{{attachment:procSnapTs.gif|procImportFs.gif}} | {{attachment:procSnapTs.gif}} |
Line 80: | Line 80: |
{{attachment:procHeadmodel.gif|procImportFs.gif}} | {{attachment:procHeadmodel.gif}} |
Line 85: | Line 85: |
{{attachment:procSources.gif|procImportFs.gif}} | {{attachment:procSources.gif}} |
Line 89: | Line 89: |
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}} |
Line 97: | Line 97: |
% Script generated by Brainstorm v3.1 (11-Jan-2013) | % Script generated by Brainstorm v3.1 (25-Jan-2013) |
Line 110: | Line 110: |
'mrifile', {'C:\Work\RawData\Tutorials\sample_raw\Anatomy', 'FsDir', [...] | 'mrifile', {'C:\Work\RawData\Tutorials\sample_raw\Anatomy', 'FsDir'}, ... |
Line 124: | Line 124: |
'datafile', {'C:\Work\RawData\Tutorials\sample_raw\Data\EF1982_somatosensory_ [...] | 'datafile', {'C:\Work\RawData\Tutorials\sample_raw\Data\EF1982_somatosensory_20111109_01_AUX-f.ds', 'CTF'}, ... |
Line 140: | Line 140: |
'timewindow', [0, 359.999167], ... | 'timewindow', [0, 359.9991667], ... |
Line 157: | Line 157: |
'timewindow', [0, 359.999167], ... 'epochtime', {[-100, 300], 'ms'}, ... |
'timewindow', [0, 359.9991667], ... 'epochtime', [-0.1, 0.3], ... |
Line 166: | Line 166: |
% Process: Remove baseline: [-100ms,0ms] | % Process: Remove baseline: [-100ms,-1ms] |
Line 170: | Line 170: |
'baseline', [-0.10001, -0.00017], ... | 'baseline', [-0.1, -0.0008333333333], ... |
Line 174: | Line 174: |
% Process: Add time offset: -4.20ms sFiles = bst_process(... 'CallProcess', 'process_timeoffset', ... sFiles, [], ... 'offset', -0.0042, ... 'overwrite', 1); |
|
Line 178: | Line 185: |
'baseline', [-0.10001, -0.000843], ... | 'baseline', [-0.1042, -0.005], ... |
Line 180: | Line 187: |
'method', 1, ... | 'method', 1, ... % Full noise covariance matrix |
Line 184: | Line 191: |
% Process: Average: By condition | % Process: Average: By condition (subject average) |
Line 188: | Line 195: |
'avgtype', 3); | 'avgtype', 3); % By condition (subject average) |
Line 194: | Line 201: |
'target', {1, {'Sensors/MRI registration', [...] 'modality', {1, {'MEG (All)', [...] 'orient', {1, {'left', 'right', 'top', 'bottom', 'front', 'back'}}, ... |
'target', 1, ... % Sensors/MRI registration 'modality', 1, ... % MEG (All) 'orient', 1, ... % left |
Line 198: | Line 205: |
'contact', '0.000, 0.100, 12', ... 'comment', 'Registration'); |
'contact_time', [0, 0.1], ... 'contact_nimage', 12, ... 'comment', 'MEG/MRI Registration'); |
Line 205: | Line 213: |
'target', {5, {'Sensors/MRI registration', [...] 'modality', {1, {'MEG (All)', [...] 'orient', {1, {'left', 'right', 'top', 'bottom', 'front', 'back'}}, ... |
'target', 5, ... % Recordings time series 'modality', 1, ... % MEG (All) 'orient', 1, ... % left |
Line 209: | Line 217: |
'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)', [...] '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', 'MEG/MRI Registration'); |
Line 228: | Line 226: |
'meg', {3, {'<none>', 'Single sphere', 'Overlapping spheres', 'OpenMEEG BEM'}}, ... 'eeg', {3, {'<none>', '3-shell sphere', 'OpenMEEG BEM'}}, ... |
'meg', 3, ... % Overlapping spheres 'eeg', 3, ... |
Line 231: | Line 229: |
'BemSelect', [0, 0, 1], ... 'BemCond', [1, 0.0125, 1], ... 'BemNames', {{'Scalp', 'Skull', 'Brain'}}, ... |
|
Line 232: | Line 233: |
'BemNames', {{'Scalp', 'Skull', 'Brain'}}, ... 'BemCond', [1, 0.0125, 1], ... 'BemSelect', [1, 1, 1], ... |
|
Line 244: | Line 242: |
'method', 1, ... | 'method', 1, ... % Minimum norm estimates (wMNE) |
Line 264: | Line 262: |
'output', 1); | 'output', 1); % Kernel only: shared |
Line 271: | Line 269: |
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. At the end, the report viewer is opened to show the status of all the processes and the screen captures. The report is saved in your home folder ($home/.brainstorm/reports). If you close this window, you can get it back with the menu File > Report viewer. |
Click on Run to start the script. As this process is taking screen captures, do not use your computer for something else at the same time: if another window covers the Brainstorm figure, it will not capture the right images. At the end, the report viewer is opened to show the status of all the processes, the information messages, the list of input and output files, and the screen captures. The report is saved in your home folder ($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}} |
Full analysis with one script
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 FreeSurfer folder
- Import recordings > Create link to raw file
- Pre-process > Sinusoid removal (notch)
- Artifacts > Detect eye blinks
- Artifacts > Compute SSP: eye blinks
- Import recordings > Import MEG/EEG : Events
- Pre-process > Remove DC 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 FreeSurfer folder
- Subject name: Subject01
- Folder to import: Select the folder sample_raw/Anatomy
- Number of vertices (cortex): 15000
- 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 recordings > Create link to raw file
Input: None; Output: Raw file
Pre-process > Sinusoid removal (notch)
Input: Raw file ; Output: Raw file (new)
Artifacts > Detect eye blinks
Input: Raw file ; Output: Raw file
Artifacts > Compute SSP: eye blinks
Input: Raw file ; Output: Raw file
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
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.
% Script generated by Brainstorm v3.1 (25-Jan-2013) % Input files FileNamesA = []; % Start a new report 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'}, ... 'nvertices', 15000, ... 'nas', [126, 215, 138], ... 'lpa', [58, 136, 121], ... 'rpa', [197, 138, 118], ... 'ac', [128, 137, 157], ... 'pc', [128, 113, 157], ... 'ih', [128, 125, 216]); % Process: Create link to raw file sFiles = bst_process(... 'CallProcess', 'process_import_data_raw', ... sFiles, [], ... 'subjectname', 'Subject01', ... 'datafile', {'C:\Work\RawData\Tutorials\sample_raw\Data\EF1982_somatosensory_20111109_01_AUX-f.ds', 'CTF'}, ... 'channelalign', 1); % Process: Sinusoid removal: 60Hz 120Hz 180Hz sFiles = bst_process(... 'CallProcess', 'process_sin_remove', ... sFiles, [], ... 'freqlist', [60, 120, 180], ... 'sensortypes', 'MEG, EEG', ... 'reverse', 1); % Process: Detect eye blinks sFiles = bst_process(... 'CallProcess', 'process_evt_detect_eog', ... sFiles, [], ... 'channelname', 'EEG058', ... 'timewindow', [0, 359.9991667], ... 'eventname', 'blink'); % Process: SSP EOG: blink sFiles = bst_process(... 'CallProcess', 'process_ssp_eog', ... sFiles, [], ... 'eventname', 'blink', ... 'sensortypes', 'MEG, MEG MAG, MEG GRAD'); % Process: Import MEG/EEG: Events sFiles = bst_process(... 'CallProcess', 'process_import_data_event', ... sFiles, [], ... 'subjectname', 'Subject01', ... 'condition', '', ... 'eventname', 'left, right', ... 'timewindow', [0, 359.9991667], ... 'epochtime', [-0.1, 0.3], ... 'createcond', 1, ... 'ignoreshort', 1, ... 'usectfcomp', 1, ... 'usessp', 1, ... 'freq', [], ... 'baseline', []); % Process: Remove baseline: [-100ms,-1ms] sFiles = bst_process(... 'CallProcess', 'process_baseline', ... sFiles, [], ... 'baseline', [-0.1, -0.0008333333333], ... 'sensortypes', 'MEG, EEG', ... 'overwrite', 1); % 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, -0.005], ... '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); % By condition (subject average) % 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', 'MEG/MRI Registration'); % Process: Compute head model sFiles = bst_process(... 'CallProcess', 'process_headmodel', ... sFiles, [], ... 'sourcespace', 1, ... 'meg', 3, ... % Overlapping spheres 'eeg', 3, ... 'openmeeg', struct(... 'BemSelect', [0, 0, 1], ... 'BemCond', [1, 0.0125, 1], ... 'BemNames', {{'Scalp', 'Skull', 'Brain'}}, ... 'BemFiles', {{}}, ... 'isAdjoint', 0, ... 'isAdaptative', 1, ... 'isSplit', 0, ... 'SplitLength', 4000)); % Process: Compute sources sFiles = bst_process(... 'CallProcess', 'process_inverse', ... sFiles, [], ... 'method', 1, ... % Minimum norm estimates (wMNE) 'wmne', struct(... 'NoiseCov', [], ... 'InverseMethod', 'wmne', ... '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, ... '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 figure, 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.