FreesurferGoodies/generatefreesurferscripts - MRC CBU Imaging Wiki

Upload page content

You can upload content for the page named below. If you change the page name, you can also upload content for another page. If the page name is empty, we derive the page name from the file name.

File to load page content from
Page name
Comment
Type the missing letters from: Lodon is th capial of nglnd

location: FreesurferGoodies / generatefreesurferscripts

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