{{{ function generatefreesurferscripts(subjectNames,cbuProjectNumber,targetDirectory) % this Matlab function generates shell scripts for the recon-all of all your subjects for a given project % INPUT % subjectNames: a cell array of the CBU identifiers (e.g. CBU111111) % cbuProjectNumber: a string of the CBU project number e.g. MR10027 % targetDirectory: the directory in which your csh scripts will end up. (e.g. '/imaging/user/yourprojectfolder/yourfreesurferscripts/') % % This will generate as many .csh files as you have subjects in your project. Once this function has completed, in a terminal run % >freesurfer % >cd $SUBJECT_DIR % >cd ../yourfreesurferscripts/ % >sh CBU111111.csh % % make sure you check out the instructions on how to set up the cbu freesurfer environment here: % http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferInformation % this is optimised for freesurfer 5.1.0 % % Ian Charest - MRC-CBSU - March 2012 rawdataPath = '/mridata/cbu/'; nSubjects = length(subjectNames); nMPRAGEimgs=192; returnHere=pwd; for subI=1:nSubjects thisSubject=subjectNames{subI}; thisCsh = [targetDirectory,filesep,thisSubject,'.csh']; fid = fopen(thisCsh,'w'); importDir = [rawdataPath,thisSubject,'_',cbuProjectNumber,filesep]; cd(importDir) temp=dir(pwd); fullimportDir=[importDir,temp(3).name,'/']; seriesDirs = dir(fullfile(fullimportDir,'*Series*')); structural=0; cd(returnHere) for seriesI=1:length(seriesDirs) currDir = [fullimportDir,seriesDirs(seriesI).name]; files = get_files(currDir,'*.dcm'); if size(files,1) == nMPRAGEimgs && structural==0 thisStruct =files(1,:); structural=1; end end fprintf(fid,['recon-all -i ' thisStruct ' -all -subjid ' thisSubject]); fclose(fid); clear fid end end function files = get_files(direc, filt) % ========================================================================= % return a list of files % filt = filter string % direc = cell array of directory names % revised 07-2011 Ian Charest if nargin~=2, error('get_files:missing inputs, Please input folder(s) and file filter.'); end%if files = []; if ischar(direc) % if direc is already a character array currDir = direc; tmp = dir(fullfile(currDir,filt)); % find all files matching f*.nii tmp = [repmat([currDir filesep],size(tmp,1),1) char(tmp.name)]; % build the full path name for these files files = char(files,tmp); else % if direc is a cell array if size(direc,1)>size(direc,2) nRuns=size(direc,1); else nRuns=size(direc,2); end for runI=1:nRuns % loop through each EPI session currDir = char(direc{runI}); tmp = dir(fullfile(currDir,filt)); % find all files matching f*.nii tmp = [repmat([currDir filesep],size(tmp,1),1) char(tmp.name)]; % build the full path name for these files files = char(files,tmp); end end files = files(~all(files'==' ')',:); end }}}