studyforrest_analysis/Preprocess.m

% Preprocess.m
%
% This funciton preprocesses data of the studyforrest data set. It searches in
% the provided directory for the anatomy and ses-movie/func directories.
%
% input:
%	dir		- directory of the subject to preprocess (if empty processes the current directory)
%   runId   - the run index to process (varies from 1 to 8)

function Preprocess(dir, runId)
    
    if (~isempty(dir) && ~strcmp(dir(end),'/'))
        dir = [dir '/'];
    end

    curDir = '';
    if (~strcmp(dir(1),'/'))
        curDir = pwd;
        curDir = [curDir '/'];
    end

    numOfVolumes = 451;
    
    anatomyScan = [curDir dir 'anatomy/highres001.nii,1'];

    scansDir = [curDir dir 'ses-movie/func/'];
    regex = [num2str(runId) '_bold.nii'];
    scans = spm_select('ExtFPList', scansDir, regex, 1:numOfVolumes);
    assert(size(scans,1) <= numOfVolumes, 'Detected more files than asked. Check if file is already preprocessed.');
    if (size(scans,1) == 0)
        warning(['Could not find any scans for directory ' dir ' and run ID ' num2str(runId)]);
        return;
    end

    % Realign - Estimate and Write (mean)
    matlabbatch{1}.spm.spatial.realign.estwrite.data{1} = cellstr(scans);
    %%
    matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;
    matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.sep = 4;
    matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;
    matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.rtm = 1;
    matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.interp = 2;
    matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];
    matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.weight = '';
    matlabbatch{1}.spm.spatial.realign.estwrite.roptions.which = [0 1];
    matlabbatch{1}.spm.spatial.realign.estwrite.roptions.interp = 4;
    matlabbatch{1}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];
    matlabbatch{1}.spm.spatial.realign.estwrite.roptions.mask = 1;
    matlabbatch{1}.spm.spatial.realign.estwrite.roptions.prefix = 'r';

    % Coregister - Estimate
    matlabbatch{2}.spm.spatial.coreg.estimate.ref = cellstr(anatomyScan);
    matlabbatch{2}.spm.spatial.coreg.estimate.source(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));
    matlabbatch{2}.spm.spatial.coreg.estimate.other(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));
    matlabbatch{2}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';
    matlabbatch{2}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];
    matlabbatch{2}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];
    matlabbatch{2}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];

    % Normalize - Estimate and write
    matlabbatch{3}.spm.spatial.normalise.estwrite.subj.vol = cellstr(anatomyScan);
    matlabbatch{3}.spm.spatial.normalise.estwrite.subj.resample(1) = cfg_dep('Coregister: Estimate: Coregistered Images', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','cfiles'));
    matlabbatch{3}.spm.spatial.normalise.estwrite.eoptions.biasreg = 0.0001;
    matlabbatch{3}.spm.spatial.normalise.estwrite.eoptions.biasfwhm = 60;
    matlabbatch{3}.spm.spatial.normalise.estwrite.eoptions.tpm = {'/home/ga58sux/workspace/spm/spm12/tpm/TPM.nii'};
    matlabbatch{3}.spm.spatial.normalise.estwrite.eoptions.affreg = 'mni';
    matlabbatch{3}.spm.spatial.normalise.estwrite.eoptions.reg = [0 0.001 0.5 0.05 0.2];
    matlabbatch{3}.spm.spatial.normalise.estwrite.eoptions.fwhm = 0;
    matlabbatch{3}.spm.spatial.normalise.estwrite.eoptions.samp = 3;
    matlabbatch{3}.spm.spatial.normalise.estwrite.woptions.bb = [-78 -112 -70
                                                                 78 76 85];
    matlabbatch{3}.spm.spatial.normalise.estwrite.woptions.vox = [3 3 3];
    matlabbatch{3}.spm.spatial.normalise.estwrite.woptions.interp = 4;
    matlabbatch{3}.spm.spatial.normalise.estwrite.woptions.prefix = 'w';
    matlabbatch{4}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Estimate & Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));

    % Smooth data
    matlabbatch{4}.spm.spatial.smooth.fwhm = [8 8 8];
    matlabbatch{4}.spm.spatial.smooth.dtype = 0;
    matlabbatch{4}.spm.spatial.smooth.im = 0;
    matlabbatch{4}.spm.spatial.smooth.prefix = 's';

    % run created matlab batch
    spm_jobman('run', matlabbatch);
end