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preproc_spm_job.m
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preproc_spm_job.m
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%-----------------------------------------------------------------------
% Job saved on 10-Aug-2022 23:57:43 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
%%
matlabbatch{1}.spm.spatial.realign.estwrite.data = {
{
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'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,151'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,152'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,153'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,154'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,155'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,156'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,157'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,158'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,159'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,160'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,161'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,162'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,163'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,164'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,165'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,166'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,167'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,168'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,169'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,170'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,171'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,172'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,173'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,174'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,175'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,176'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,177'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,178'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,179'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,180'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,181'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,182'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,183'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,184'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,185'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,186'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,187'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,188'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,189'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,190'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,191'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,192'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,193'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,194'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,195'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,196'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,197'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,198'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,199'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,200'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,201'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,202'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,203'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,204'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,205'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,206'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,207'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,208'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,209'
'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\fmri.nii,210'
}
}';
%%
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 = 4;
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 = [2 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';
matlabbatch{2}.spm.spatial.coreg.estimate.ref(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.source = {'C:\Users\kasperla\OneDrive - UHN\Grants\2022\CIHR_Fidel\Pilot\results\sub-02\struct.nii,1'};
matlabbatch{2}.spm.spatial.coreg.estimate.other = {''};
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];
matlabbatch{3}.spm.spatial.preproc.channel.vols(1) = cfg_dep('Coregister: Estimate: Coregistered Images', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','cfiles'));
matlabbatch{3}.spm.spatial.preproc.channel.biasreg = 0.001;
matlabbatch{3}.spm.spatial.preproc.channel.biasfwhm = 60;
matlabbatch{3}.spm.spatial.preproc.channel.write = [1 1];
matlabbatch{3}.spm.spatial.preproc.tissue(1).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,1'};
matlabbatch{3}.spm.spatial.preproc.tissue(1).ngaus = 1;
matlabbatch{3}.spm.spatial.preproc.tissue(1).native = [1 0];
matlabbatch{3}.spm.spatial.preproc.tissue(1).warped = [0 1];
matlabbatch{3}.spm.spatial.preproc.tissue(2).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,2'};
matlabbatch{3}.spm.spatial.preproc.tissue(2).ngaus = 1;
matlabbatch{3}.spm.spatial.preproc.tissue(2).native = [1 0];
matlabbatch{3}.spm.spatial.preproc.tissue(2).warped = [0 1];
matlabbatch{3}.spm.spatial.preproc.tissue(3).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,3'};
matlabbatch{3}.spm.spatial.preproc.tissue(3).ngaus = 2;
matlabbatch{3}.spm.spatial.preproc.tissue(3).native = [1 0];
matlabbatch{3}.spm.spatial.preproc.tissue(3).warped = [0 1];
matlabbatch{3}.spm.spatial.preproc.tissue(4).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,4'};
matlabbatch{3}.spm.spatial.preproc.tissue(4).ngaus = 3;
matlabbatch{3}.spm.spatial.preproc.tissue(4).native = [1 0];
matlabbatch{3}.spm.spatial.preproc.tissue(4).warped = [0 0];
matlabbatch{3}.spm.spatial.preproc.tissue(5).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,5'};
matlabbatch{3}.spm.spatial.preproc.tissue(5).ngaus = 4;
matlabbatch{3}.spm.spatial.preproc.tissue(5).native = [1 0];
matlabbatch{3}.spm.spatial.preproc.tissue(5).warped = [0 0];
matlabbatch{3}.spm.spatial.preproc.tissue(6).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,6'};
matlabbatch{3}.spm.spatial.preproc.tissue(6).ngaus = 2;
matlabbatch{3}.spm.spatial.preproc.tissue(6).native = [0 0];
matlabbatch{3}.spm.spatial.preproc.tissue(6).warped = [0 0];
matlabbatch{3}.spm.spatial.preproc.warp.mrf = 1;
matlabbatch{3}.spm.spatial.preproc.warp.cleanup = 1;
matlabbatch{3}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{3}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{3}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{3}.spm.spatial.preproc.warp.samp = 3;
matlabbatch{3}.spm.spatial.preproc.warp.write = [0 1];
matlabbatch{3}.spm.spatial.preproc.warp.vox = NaN;
matlabbatch{3}.spm.spatial.preproc.warp.bb = [NaN NaN NaN
NaN NaN NaN];
matlabbatch{4}.spm.spatial.preproc.channel.vols(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));
matlabbatch{4}.spm.spatial.preproc.channel.biasreg = 0.001;
matlabbatch{4}.spm.spatial.preproc.channel.biasfwhm = 60;
matlabbatch{4}.spm.spatial.preproc.channel.write = [1 1];
matlabbatch{4}.spm.spatial.preproc.tissue(1).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,1'};
matlabbatch{4}.spm.spatial.preproc.tissue(1).ngaus = 1;
matlabbatch{4}.spm.spatial.preproc.tissue(1).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(1).warped = [0 1];
matlabbatch{4}.spm.spatial.preproc.tissue(2).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,2'};
matlabbatch{4}.spm.spatial.preproc.tissue(2).ngaus = 1;
matlabbatch{4}.spm.spatial.preproc.tissue(2).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(2).warped = [0 1];
matlabbatch{4}.spm.spatial.preproc.tissue(3).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,3'};
matlabbatch{4}.spm.spatial.preproc.tissue(3).ngaus = 2;
matlabbatch{4}.spm.spatial.preproc.tissue(3).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(3).warped = [0 1];
matlabbatch{4}.spm.spatial.preproc.tissue(4).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,4'};
matlabbatch{4}.spm.spatial.preproc.tissue(4).ngaus = 3;
matlabbatch{4}.spm.spatial.preproc.tissue(4).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(4).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(5).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,5'};
matlabbatch{4}.spm.spatial.preproc.tissue(5).ngaus = 4;
matlabbatch{4}.spm.spatial.preproc.tissue(5).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(5).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(6).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,6'};
matlabbatch{4}.spm.spatial.preproc.tissue(6).ngaus = 2;
matlabbatch{4}.spm.spatial.preproc.tissue(6).native = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(6).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.warp.mrf = 1;
matlabbatch{4}.spm.spatial.preproc.warp.cleanup = 1;
matlabbatch{4}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{4}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{4}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{4}.spm.spatial.preproc.warp.samp = 3;
matlabbatch{4}.spm.spatial.preproc.warp.write = [0 1];
matlabbatch{4}.spm.spatial.preproc.warp.vox = NaN;
matlabbatch{4}.spm.spatial.preproc.warp.bb = [NaN NaN NaN
NaN NaN NaN];
matlabbatch{5}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));
matlabbatch{5}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70
78 76 85];
matlabbatch{5}.spm.spatial.normalise.write.woptions.vox = [1 1 1];
matlabbatch{5}.spm.spatial.normalise.write.woptions.interp = 4;
matlabbatch{5}.spm.spatial.normalise.write.woptions.prefix = 'w';
matlabbatch{6}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));
matlabbatch{6}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));
matlabbatch{6}.spm.spatial.normalise.write.subj.resample(2) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));
matlabbatch{6}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70
78 76 85];
matlabbatch{6}.spm.spatial.normalise.write.woptions.vox = [1 1 1];
matlabbatch{6}.spm.spatial.normalise.write.woptions.interp = 4;
matlabbatch{6}.spm.spatial.normalise.write.woptions.prefix = 'w';
matlabbatch{7}.spm.spatial.smooth.data(1) = cfg_dep('Realign: Estimate & Reslice: Resliced Images (Sess 1)', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','rfiles'));
matlabbatch{7}.spm.spatial.smooth.fwhm = [3 3 3];
matlabbatch{7}.spm.spatial.smooth.dtype = 0;
matlabbatch{7}.spm.spatial.smooth.im = 0;
matlabbatch{7}.spm.spatial.smooth.prefix = 's';