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tools:source_localization [2026/11/09 16:14] – created sdm63tools:source_localization [2026/11/09 16:38] (current) – sdm63
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 Running/ installing brainstorm will automatically make a brainstorm_db folder in the same folder where brainstorm3 is saved (in my case resources) \\ Running/ installing brainstorm will automatically make a brainstorm_db folder in the same folder where brainstorm3 is saved (in my case resources) \\
  
-== Brainstorm Organization ==+=== Brainstorm Organization ===
   * Each subject is then saved as a protocol that is then saved in that database folder    * Each subject is then saved as a protocol that is then saved in that database folder 
   * With each protocol there is an anat and data folder   * With each protocol there is an anat and data folder
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     * data: your brain data      * data: your brain data 
       * contains eeg files that you load in        * contains eeg files that you load in 
 +\\
 +
 +=== Brainstorm Scripts ===
 +  * I have one script for each task epoch (fix, delay, resting state, etc)
 +  * Sets the necessary paths to the freesurfer folders, list of glasser parcellations, merge 7t, and preprocessed data 
 +  * We need the subject folders that have 'long' in the title so it checks for that and if yes, moves on 
 +<code> if contains(FSsubfolder,'long') </code>
 + 
 +  * Define the subject folder (protocol), DBfolder is the brainstorm_db, and then I named it sourceLocal_beamforming_ subjectID based on their MRI date, not eeg date to match the freesurfer file
 +<code> subjectDBfolder = [DBfolder '/sourceLocal_beamforming_' SubjectNameMRI]; </code> 
 +
 +  * Here we are setting the protocol name
 +  * The iProtocol bst_get checks to see the protocol already exists in the database
 +  * If no (iProtocol is empty), then create protocol, and add the subject within it
 +    * That just creates a blank subject line in the protocol to then fill with the anat and data
 +  * If the protocol does exist, then load it and set it as the current protocol
 +
 +<code> 
 +ProtocolName = sprintf('sourceLocal_beamforming_%s', SubjectNameMRI);
 +iProtocol = bst_get('Protocol', ProtocolName);
 +
 +if isempty(iProtocol)
 +
 +    gui_brainstorm('CreateProtocol', ProtocolName, 0, 0);
 +    db_add_subject(SubjectNameMRI, [], 1);
 +
 +else
 +
 +    gui_brainstorm('SetCurrentProtocol', iProtocol);
 +
 +end 
 +
 +</code>
 +
 +
 +  * bst_get('ProtocolStudies') pulls out the studies within one protocol 
 +    * A study is like each EEG file you have loaded into that protocol, so everyone should have fix, delays, and rest
 +  * But this code below checks to see if fix (or delay or rest or whatever what you're running) already exists and removes it (cause maybe you wanna redo it)
 +
 +<code>
 +sStudies = bst_get('ProtocolStudies');
 +
 +for iStudy = 1:length(sStudies.Study)
 +studyName = sStudies.Study(iStudy).Name;
 +
 +    if contains(studyName, 'fix')
 +
 +        fprintf('Deleting study: %s\n', studyName);
 +        db_delete_studies(iStudy);
 +
 +    end
 +
 +end
 +
 +</code>
 +
 +  * Find the lunaID
 +  * Find the MRI date
 +  * Find the row in merge 7t with the corresponding lunaID and MRI date
 +  * Using that row, find the EEG date
 +  * Create the path to the corresponding EEG file
 +
 +<code>
 +luna = str2double(SubjectNameMRI(1:5));
 +MRIdate = str2double(SubjectNameMRI(7:14));
 +                    
 +rowIdx = merge7t(:,1) == luna & merge7t(:,4) == MRIdate;
 +
 +if any(rowIdx)
 +
 +   eeg_date = merge7t(rowIdx,5);
 +
 +   pattern = sprintf('%s_%s*_rerefwhole_ICA_icapru.set', string(luna), string(eeg_date));
 +   files = dir(fullfile(EEGfolder, pattern));
 +
 +   EEGpath = fullfile(EEGfolder, files.name);
 +
 +else
 +
 +   continue
 +
 +end
 +</code>