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Author: imnanxu

partialbrain_preprocessing_pipeline2020_nx/epi_split.m

@@ -4,7 +4,7 @@ function epi_split(subjectdir, filename, scans_subj, prefix, fsldir, Ntime)
 cd(subjectdir);
 system('pwd');
 
-for scan_num=1:length(scans_subj)
+parfor scan_num=1:length(scans_subj)
     cmd = [fsldir 'fslroi ' filename ' ' char(scans_subj(scan_num)) ...
         prefix ' ' num2str(Ntime * (scan_num - 1)) ' ' num2str(Ntime)];
     disp(cmd);

partialbrain_preprocessing_pipeline2020_nx/preprocess_functional_parcellation_zscore.m

@@ -14,38 +14,20 @@ function preprocess_functional_parcellation_zscore(subjectdir, atlas_filename, f
 T = datetime('now'); time = whatsthetime(T);
 fprintf([time,sub, scan ': ','Functional Parcellation & Zcoring ... '])
 
-%% Parcellation & Z-scoring   
-nii_tmp=load_untouch_nii(atlas_filename);
-TMP=nii_tmp.img; ROI_ids=unique(TMP(:));
- 
+%% Parcellation & Z-scoring    
 filename1=[filename, '.nii.gz'];
+cmd=['3dROIstats -mask ' atlas_filename ' -nomeanout -nzmean -quiet ' ...
+     filename1 '  > ' filename '_seed_' atlas '.txt']; system(cmd);
+ts_parcel=dlmread([filename '_seed_' atlas '.txt'])'; ts_zscore=zscore(ts_parcel,[],2);
 
-% cmd=['3dROIstats -mask ' atlas_filename ' -nomeanout -nobriklab -nzmean -quiet ' ...
-%      filename1 '  > ' filename '_seed_' atlas '.txt'];
-% system(cmd);
+cmd=['3dROIstats -mask ' atlas_filename ' -nomeanout -nzvoxels -quiet ' ...
+     atlas_filename '  > ' atlas '_voxelNum.txt']; system(cmd); 
+voxel_per_roi1=dlmread([atlas '_voxelNum.txt'])';
 
-nii_img=load_untouch_nii(filename1);
-IMG0=nii_img.img; %IMG_parcel=zeros(size(IMG0)); IMG_zscore=zeros(size(IMG0));
-Ntime=size(IMG0,4);
-
-ts_parcel=zeros(length(ROI_ids)-1,Ntime);
-ts_zscore=zeros(length(ROI_ids)-1,Ntime);
-
-voxel_per_roi1=zeros(length(ROI_ids)-1,1);
-voxel_per_roi2=zeros(length(ROI_ids)-1,1);
-parfor roi_ct=1:length(ROI_ids)-1
-   mask_roi=zeros(size(TMP));
-   roi=ROI_ids(roi_ct+1);
-   mask_roi(TMP==roi)=1;
-   voxel_per_roi1(roi_ct)=length(nonzeros(mask_roi));
-   
-   IMG_masked=bsxfun(@times, mask_roi, IMG0);
-   v_roi = nonzeros(IMG_masked(:,:,:,1));  
-   voxel_per_roi2(roi_ct)=length(v_roi);
-   IMG_masked_2D=reshape(nonzeros(IMG_masked),[voxel_per_roi2(roi_ct), Ntime]);
-   ts_parcel(roi_ct,:)=mean(IMG_masked_2D,1);      
-   ts_zscore(roi_ct,:) = zscore(ts_parcel(roi_ct,:));   
-end
+cmd=['3dROIstats -mask ' atlas_filename ' -nomeanout -nzvoxels -quiet ' ...
+     filename1 '[0]  > ' filename '_voxelNum_' atlas '.txt']; system(cmd);
+voxel_per_roi2=dlmread([filename '_voxelNum_' atlas '.txt'])';
 voxel_per_roi=[voxel_per_roi1, voxel_per_roi2];
+
 save([filename '_on_parcel_' atlas '.mat'],'ts_parcel', 'ts_zscore','voxel_per_roi');
 fprintf('Done\n')