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preproc_minimal_spm_job.m
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preproc_minimal_spm_job.m
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%-----------------------------------------------------------------------
% Job saved on 20-Nov-2022 12:56:47 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
%%
matlabbatch{1}.spm.spatial.realign.estwrite.data = {
{
'nifti/fmri.nii,1'
'nifti/fmri.nii,2'
'nifti/fmri.nii,3'
'nifti/fmri.nii,4'
'nifti/fmri.nii,5'
'nifti/fmri.nii,6'
'nifti/fmri.nii,7'
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'nifti/fmri.nii,9'
'nifti/fmri.nii,10'
'nifti/fmri.nii,11'
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'nifti/fmri.nii,20'
'nifti/fmri.nii,21'
'nifti/fmri.nii,22'
'nifti/fmri.nii,23'
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}
}';
%%
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 = {'nifti/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.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));
matlabbatch{4}.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{4}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70
78 76 85];
matlabbatch{4}.spm.spatial.normalise.write.woptions.vox = [1 1 1];
matlabbatch{4}.spm.spatial.normalise.write.woptions.interp = 4;
matlabbatch{4}.spm.spatial.normalise.write.woptions.prefix = 'w';
matlabbatch{5}.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{5}.spm.spatial.smooth.fwhm = [3 3 3];
matlabbatch{5}.spm.spatial.smooth.dtype = 0;
matlabbatch{5}.spm.spatial.smooth.im = 0;
matlabbatch{5}.spm.spatial.smooth.prefix = 's';