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Version: brainstorm3
Package is in Shane/resources/brainstorm3
Need to add its path to matlab and then just run the command brainstorm
Running/ installing brainstorm will automatically make a brainstorm_db folder in the same folder where brainstorm3 is saved (in my case resources)

• 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
  • anat: anatomy
    • contains the anatomy files that were uploaded (from their freesurfer output)
  • data: your brain data
    • contains eeg files that you load in

• 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

 if contains(FSsubfolder,'long') 

• 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

 subjectDBfolder = [DBfolder '/sourceLocal_beamforming_' SubjectNameMRI]; 

• 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

 
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 

• 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)

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

• 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

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