Coded added to script02_writeMNI.m, plus other minor changes

script02_writeMNI.m
- added 2 blocks of code: writes MNI152 positions to a new electrodes.tsv (using SPM forward deformation fields), and writes MNI305 positions to a new electrodes.tsv using fsaverage

gitignore
- added ignores for *.asv and personalDataPath.m

script01_preprocNSDMef
- elecPath -> now elecsPath

.gitignore

@@ -3,3 +3,4 @@ output/
 personalDataPath.m
 .DS_Store
 */.DS_Store
+*.asv

script01_preprocNSDMef.m

@@ -10,7 +10,7 @@
 addpath('functions');
 
 % subject to preprocess
-ss = 1;
+ss = 17;
 sub_label = sprintf('%02d', ss);
 
 ses_label = 'ieeg01';
@@ -20,8 +20,8 @@
 task_list = readtable(fullfile(localDataPath.input,['sub-' sub_label],['ses-' ses_label],['sub-' sub_label '_ses-' ses_label '_scans.tsv']), 'FileType', 'text', 'Delimiter', '\t', 'TreatAsEmpty', 'n/a');
 
 % electrodes path (to exclude electrodes on the SOZ)
-elecPath = fullfile(localDataPath.input, ['sub-' sub_label], ['ses-' ses_label], 'ieeg', ['sub-' sub_label '_ses-' ses_label '_electrodes.tsv']);
-elecs = ieeg_readtableRmHyphens(elecPath);
+elecsPath = fullfile(localDataPath.input, ['sub-' sub_label], ['ses-' ses_label], 'ieeg', ['sub-' sub_label '_ses-' ses_label '_electrodes.tsv']);
+elecs = ieeg_readtableRmHyphens(elecsPath);
 
 % For all possible runs, set data_info
 data_info = [];
@@ -253,8 +253,8 @@
 
 %% render and plot noise ceiling SNR
 
-elecPath = fullfile(localDataPath.input, ['sub-' sub_label], ['ses-' ses_label], 'ieeg', ['sub-' sub_label '_ses-' ses_label '_electrodes.tsv']);
-elecs = ieeg_readtableRmHyphens(elecPath);
+elecsPath = fullfile(localDataPath.input, ['sub-' sub_label], ['ses-' ses_label], 'ieeg', ['sub-' sub_label '_ses-' ses_label '_electrodes.tsv']);
+elecs = ieeg_readtableRmHyphens(elecsPath);
 
 name = all_channels.name;
 all_channels_table = table(name);

script02_writeMNI.m

@@ -1,24 +1,58 @@
+%% This script calculates MNI152 and MNI305 positions each subject and saves them
 
-clear all
 localDataPath = setLocalDataPath(1); % runs local PersonalDataPath (gitignored)
 addpath('functions');
 
-subjects = {'01','02','03','04','05','06'};
+ss = 17;
+sub_label = sprintf('%02d', ss);
 
-ss = 4;
-sub_label = subjects{ss};
 ses_label = 'ieeg01';
-
 outdir = fullfile(localDataPath.output,'derivatives','preproc_car',['sub-' sub_label]);
 
-% load(fullfile(outdir, ['sub-' sub_label '_desc-preprocCAR_ieeg.mat']), 'tt', 'srate', 'Mdata', 'eventsST', 'all_channels');
-load(fullfile(outdir, ['sub-' sub_label '_desc-preprocCARBB_ieeg.mat']), 'tt', 'srate', 'Mbb', 'eventsST', 'all_channels');
-readtable(fullfile(outdir, ['sub-' sub_label '_desc-preprocCAR_events.tsv']), 'FileType', 'text', 'Delimiter', '\t', 'TreatAsEmpty', 'n/a');
+% load electrodes
+elecsPath = fullfile(localDataPath.input, ['sub-' sub_label], ['ses-' ses_label], 'ieeg', ['sub-' sub_label '_ses-' ses_label '_electrodes.tsv']);
+elecs = ieeg_readtableRmHyphens(elecsPath);
+elecmatrix = [elecs.x, elecs.y, elecs.z];
+
+%% Get and save MNI152 positions to electrodesMni152.tsv (volumetric, SPM12)
+
+% locate forward deformation field from SPM. There are variabilities in session name, so we use dir to find a matching one
+niiPath = dir(fullfile(localDataPath.input, 'sourcedata', 'spm_forward_deformation_fields', sprintf('sub-%s_ses-*_T1w_acpc.nii', sub_label)));
+assert(length(niiPath) == 1, 'Error: did not find exactly one match in sourcedata T1w MRI'); % check for only one unique match
+niiPath = fullfile(niiPath.folder, niiPath.name);
+
+% create a location in derivatives to save the transformed electrode images
+rootdirMni = fullfile(localDataPath.input, 'derivatives', 'MNI152_electrode_transformations', sprintf('sub-%s', sub_label));
+mkdir(rootdirMni);
+
+% calculate MNI152 coordinates for electrodes
+xyzMni152 = ieeg_getXyzMni(elecmatrix, niiPath, rootdirMni);
+
+% save as separate MNI 152 electrodes table
+elecsMni152Path = fullfile(localDataPath.input, ['sub-' sub_label], ['ses-' ses_label], 'ieeg', ['sub-' sub_label '_ses-' ses_label '_space-' 'MNI152NLin2009' '_electrodes.tsv']);
+elecsMni152 = elecs;
+elecsMni152.x = xyzMni152(:, 1); elecsMni152.y = xyzMni152(:, 2); elecsMni152.z = xyzMni152(:, 3);
+writetable(elecsMni152, elecsMni152Path, 'FileType', 'text', 'Delimiter', '\t');
+
+fprintf('Saved to %s\n', elecsMni152Path);
+
+%% Get and save MNI305 positions (through fsaverage)
+
+% FS dir of current subject
+FSdir = fullfile(localDataPath.input, 'sourcedata', 'freesurfer', sprintf('sub-%s', sub_label));
+FSsubjectsdir = fullfile(FSdir, '..');
 
-%% need to get MNI positions first
+% calculate MNI305 coordinates for electrodes
+[xyzMni305, vertIdxFsavg, minDists, surfUsed] = ieeg_mni305ThroughFsSphere(elecmatrix, elecs.hemisphere, FSdir, FSsubjectsdir, 'closest', 5);
 
-% mni_coords = ieeg_mni305ThroughFsSphere(elecmatrix,hemi,FSdir,FSsubjectsdir)
+% save as separate MNI 305 electrodes table
+elecsMni305Path = fullfile(localDataPath.input, ['sub-' sub_label], ['ses-' ses_label], 'ieeg', ['sub-' sub_label '_ses-' ses_label '_space-' 'MNI305' '_electrodes.tsv']);
+elecsMni305 = elecs;
+elecsMni305.x = xyzMni305(:, 1); elecsMni305.y = xyzMni305(:, 2); elecsMni305.z = xyzMni305(:, 3);
+elecsMni305.vertex_fsaverage = vertIdxFsavg; % also add a column to indicate vertex on fsavg, so we can easily get position for inflated brain
+writetable(elecsMni305, elecsMni305Path, 'FileType', 'text', 'Delimiter', '\t');
 
+fprintf('Saved to %s\n', elecsMni305Path);
 
 %% Normalize bb power per run
 
@@ -66,8 +100,8 @@
 
 %% render and plot noise ceiling SNR
 
-elecPath = fullfile(localDataPath.input, ['sub-' sub_label], ['ses-' ses_label], 'ieeg', ['sub-' sub_label '_ses-' ses_label '_electrodes.tsv']);
-elecs = ieeg_readtableRmHyphens(elecPath);
+elecsPath = fullfile(localDataPath.input, ['sub-' sub_label], ['ses-' ses_label], 'ieeg', ['sub-' sub_label '_ses-' ses_label '_electrodes.tsv']);
+elecs = ieeg_readtableRmHyphens(elecsPath);
 
 name = all_channels.name;
 all_channels_table = table(name);