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Tutorial: Add cMEM estimates in tutorials (#721)
* Update `tutorial_epilepsy.m` * Create `tutorial_BEst.m` --------- Co-authored-by: rcassani <[email protected]>
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| function tutorial_BEst(tutorial_dir, reports_dir) | ||
| % TUTORIAL_BEST: Script that runs all the Brain Entropy in space and time introduction tutorials. | ||
| % | ||
| % CORRESPONDING ONLINE TUTORIAL: | ||
| % https://neuroimage.usc.edu/brainstorm/Tutorials/TutBEst | ||
| % | ||
| % INPUTS: | ||
| % - tutorial_dir : Directory where the sample_introduction.zip file has been unzipped | ||
| % - reports_dir : Directory where to save the execution report (instead of displaying it) | ||
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| % @============================================================================= | ||
| % This function is part of the Brainstorm software: | ||
| % https://neuroimage.usc.edu/brainstorm | ||
| % | ||
| % Copyright (c) University of Southern California & McGill University | ||
| % This software is distributed under the terms of the GNU General Public License | ||
| % as published by the Free Software Foundation. Further details on the GPLv3 | ||
| % license can be found at http://www.gnu.org/copyleft/gpl.html. | ||
| % | ||
| % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE | ||
| % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY | ||
| % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF | ||
| % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY | ||
| % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE. | ||
| % | ||
| % For more information type "brainstorm license" at command prompt. | ||
| % =============================================================================@ | ||
| % | ||
| % Author: Edouard Delaire, 2024 | ||
| % Raymundo Cassani, 2024 | ||
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| % ===== FILES TO IMPORT ===== | ||
| % Output folder for reports | ||
| if (nargin < 2) || isempty(reports_dir) || ~isdir(reports_dir) | ||
| reports_dir = []; | ||
| end | ||
| % Folder in which the Introduction tutorial dataset is unzipped (if needed) | ||
| if (nargin == 0) || isempty(tutorial_dir) || ~file_exist(tutorial_dir) | ||
| tutorial_dir = []; | ||
| end | ||
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| % Re-inialize random number generator | ||
| if (bst_get('MatlabVersion') >= 712) | ||
| rng('default'); | ||
| end | ||
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| %% ===== VERIFY REQUIRED PROTOCOL ===== | ||
| ProtocolName = 'TutorialIntroduction'; | ||
| SubjectName = 'Subject01'; | ||
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| iProtocolIntroduction = bst_get('Protocol', ProtocolName); | ||
| if isempty(iProtocolIntroduction) | ||
| % Produce the Introduction protocol | ||
| tutorial_introduction(tutorial_dir, reports_dir) | ||
| else | ||
| % Select input protocol | ||
| gui_brainstorm('SetCurrentProtocol', iProtocolIntroduction); | ||
| end | ||
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| %% ===== REQUIRED PLUGIN ===== | ||
| % Install and Load Brain Entropy plugin | ||
| [isInstalled, errMsg] = bst_plugin('Install', 'brainentropy'); | ||
| if ~isInstalled | ||
| error(errMsg); | ||
| end | ||
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| %% ===== FIND FILES ===== | ||
| % Process: Select recordings in: Subject01/S01_AEF_20131218_01_600Hz_notch | ||
| sFiles01 = bst_process('CallProcess', 'process_select_files_data', [], [], ... | ||
| 'subjectname', SubjectName, ... | ||
| 'condition', 'S01_AEF_20131218_01_600Hz_notch', ... | ||
| 'includebad', 0); | ||
| % Process: Select file comments with tag: deviant | ||
| sFilesAvgDeviant01 = bst_process('CallProcess', 'process_select_tag', sFiles01, [], ... | ||
| 'tag', 'Avg: deviant', ... | ||
| 'search', 2, ... % Search the file comments | ||
| 'select', 1); % Select only the files with the tag | ||
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| %% ===== HEAD MODEL ===== | ||
| disp([10 'BST> Head model' 10]); | ||
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| % Process: Generate BEM surfaces | ||
| bst_process('CallProcess', 'process_generate_bem', [], [], ... | ||
| 'subjectname', SubjectName, ... | ||
| 'nscalp', 1922, ... | ||
| 'nouter', 1922, ... | ||
| 'ninner', 1922, ... | ||
| 'thickness', 4, ... | ||
| 'method', 'brainstorm'); | ||
| % Process: Compute head model | ||
| bst_process('CallProcess', 'process_headmodel', sFilesAvgDeviant01, [], ... | ||
| 'sourcespace', 1, ... % Cortex surface | ||
| 'meg', 4, ... % OpenMEEG BEM | ||
| 'openmeeg', struct(... | ||
| 'BemSelect', [0, 0, 1], ... | ||
| 'BemCond', [0.33, 0.0165, 0.33], ... | ||
| 'BemNames', {{'Scalp', 'Skull', 'Brain'}}, ... | ||
| 'BemFiles', {{}}, ... | ||
| 'isAdjoint', 1, ... | ||
| 'isAdaptative', 1, ... | ||
| 'isSplit', 0, ... | ||
| 'SplitLength', 4000)); | ||
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| %% ===== SOURCE ESTIMATION ===== | ||
| % coherent Maximum Entropy on the Mean (cMEM) | ||
| disp([10 'BST> Source estimation using cMEM' 10]); | ||
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| % Process: Compute sources: BEst | ||
| mem_option = be_pipelineoptions(be_main, 'cMEM'); | ||
| mem_option.optional = struct_copy_fields(mem_option.optional, ... | ||
| struct(... | ||
| 'TimeSegment', [0.05, 0.15], ... | ||
| 'BaselineType', {{'within-data'}}, ... | ||
| 'Baseline', [], ... | ||
| 'BaselineHistory', {{'within'}}, ... | ||
| 'BaselineSegment', [-0.1, 0], ... | ||
| 'groupAnalysis', 0, ... | ||
| 'display', 0)); | ||
| sAvgSrcMEM = bst_process('CallProcess', 'process_inverse_mem', sFilesAvgDeviant01, [], ... | ||
| 'comment', 'MEM', ... | ||
| 'mem', struct('MEMpaneloptions', mem_option), ... | ||
| 'sensortypes', 'MEG'); | ||
| % Process: Snapshot: Sources (one time) | ||
| bst_process('CallProcess', 'process_snapshot', sAvgSrcMEM, [], ... | ||
| 'target', 8, ... % Sources (one time) | ||
| 'modality', 1, ... % MEG (All) | ||
| 'orient', 1, ... % left | ||
| 'time', 83.3*1e-3, ... | ||
| 'threshold', 0, ... | ||
| 'Comment', 'Average Deviant (cMEM)'); | ||
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| % wavelet Maximum Entropy on the Mean (wMEM) | ||
| disp([10 'BST> Source estimation using WMEM' 10]); | ||
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| % Process: Compute sources: BEst | ||
| wMEM_options = be_pipelineoptions(be_main, 'wMEM'); | ||
| wMEM_options.optional = struct_copy_fields(wMEM_options.optional, ... | ||
| struct(... | ||
| 'TimeSegment', [0.05, 0.15], ... | ||
| 'BaselineType', {{'within-data'}}, ... | ||
| 'Baseline', [], ... | ||
| 'BaselineHistory', {{'within'}}, ... | ||
| 'BaselineSegment', [-0.1, 0], ... | ||
| 'groupAnalysis', 0, ... | ||
| 'display', 0)); | ||
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| % 1. Localizing only scale 4: | ||
| wMEM_options.wavelet.selected_scales = [4]; | ||
| sAvgSrwMEM_scale4 = bst_process('CallProcess', 'process_inverse_mem', sFilesAvgDeviant01, [], ... | ||
| 'comment', 'MEM', ... | ||
| 'mem', struct( 'MEMpaneloptions', wMEM_options), ... | ||
| 'sensortypes', 'MEG'); | ||
| % Process: Snapshot: Sources (one time) | ||
| bst_process('CallProcess', 'process_snapshot', sAvgSrwMEM_scale4, [], ... | ||
| 'target', 8, ... % Sources (one time) | ||
| 'modality', 1, ... % MEG (All) | ||
| 'orient', 1, ... % left | ||
| 'time', 83.3*1e-3, ... | ||
| 'threshold', 0, ... | ||
| 'Comment', 'Average Deviant (wMEM - scale 4)'); | ||
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| % 2. Localizing only scale 5: | ||
| wMEM_options.wavelet.selected_scales = [5]; | ||
| sAvgSrwMEM_scale5 = bst_process('CallProcess', 'process_inverse_mem', sFilesAvgDeviant01, [], ... | ||
| 'comment', 'MEM', ... | ||
| 'mem', struct( 'MEMpaneloptions', wMEM_options), ... | ||
| 'sensortypes', 'MEG'); | ||
| % Process: Snapshot: Sources (one time) | ||
| bst_process('CallProcess', 'process_snapshot', sAvgSrwMEM_scale5, [], ... | ||
| 'target', 8, ... % Sources (one time) | ||
| 'modality', 1, ... % MEG (All) | ||
| 'orient', 1, ... % left | ||
| 'time', 83.3*1e-3, ... | ||
| 'threshold', 0, ... | ||
| 'Comment', 'Average Deviant (wMEM - scale 5 )'); | ||
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| % 3. Localizing all scales: | ||
| wMEM_options.wavelet.selected_scales = [1,2,3,4,5]; | ||
| sAvgSrwMEM_scaleAll = bst_process('CallProcess', 'process_inverse_mem', sFilesAvgDeviant01, [], ... | ||
| 'comment', 'MEM', ... | ||
| 'mem', struct( 'MEMpaneloptions', wMEM_options), ... | ||
| 'sensortypes', 'MEG'); | ||
| % Process: Snapshot: Sources (one time) | ||
| bst_process('CallProcess', 'process_snapshot', sAvgSrwMEM_scaleAll, [], ... | ||
| 'target', 8, ... % Sources (one time) | ||
| 'modality', 1, ... % MEG (All) | ||
| 'orient', 1, ... % left | ||
| 'time', 83.3*1e-3, ... | ||
| 'threshold', 0, ... | ||
| 'Comment', 'Average Deviant (wMEM - all scale)'); | ||
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| %% ===== SAVE REPORT ===== | ||
| % Save and display report | ||
| ReportFile = bst_report('Save', []); | ||
| if ~isempty(reports_dir) && ~isempty(ReportFile) | ||
| bst_report('Export', ReportFile, reports_dir); | ||
| else | ||
| bst_report('Open', ReportFile); | ||
| end | ||
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| disp([10 'BST> tutorial_BEst: Done.' 10]); |
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