====== Source Localization ======

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) \\

=== Brainstorm Organization ===
  * 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 
\\

=== 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>