preproc_minimal_no_struct_spm_job.m

%-----------------------------------------------------------------------
% Job saved on 20-Nov-2022 13:01:56 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\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,321'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,322'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,323'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,324'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,325'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,326'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,327'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,328'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,329'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,330'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,331'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,332'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,333'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,334'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,335'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,336'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,337'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,338'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,339'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,340'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,341'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,342'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,343'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,344'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,345'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,346'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,347'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,348'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,349'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,350'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,351'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,352'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,353'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,354'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,355'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,356'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,357'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,358'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,359'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,360'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,361'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,362'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,363'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,364'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,365'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,366'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,367'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,368'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,369'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,370'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,371'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,372'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,373'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,374'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,375'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,376'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,377'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,378'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,379'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,380'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,381'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,382'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,383'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,384'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,385'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,386'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,387'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,388'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,389'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,390'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,391'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,392'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,393'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,394'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,395'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,396'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,397'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,398'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,399'
                                                    'C:\Users\kasperla\OneDrive - UHN\Collaborations\PhysIO\CUBRICTalk\results\sub-01\nifti\fmri.nii,400'
                                                    }
                                                    }';
%%
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.preproc.channel.vols(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));
matlabbatch{2}.spm.spatial.preproc.channel.biasreg = 0.001;
matlabbatch{2}.spm.spatial.preproc.channel.biasfwhm = 60;
matlabbatch{2}.spm.spatial.preproc.channel.write = [1 1];
matlabbatch{2}.spm.spatial.preproc.tissue(1).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,1'};
matlabbatch{2}.spm.spatial.preproc.tissue(1).ngaus = 1;
matlabbatch{2}.spm.spatial.preproc.tissue(1).native = [1 0];
matlabbatch{2}.spm.spatial.preproc.tissue(1).warped = [0 1];
matlabbatch{2}.spm.spatial.preproc.tissue(2).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,2'};
matlabbatch{2}.spm.spatial.preproc.tissue(2).ngaus = 1;
matlabbatch{2}.spm.spatial.preproc.tissue(2).native = [1 0];
matlabbatch{2}.spm.spatial.preproc.tissue(2).warped = [0 1];
matlabbatch{2}.spm.spatial.preproc.tissue(3).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,3'};
matlabbatch{2}.spm.spatial.preproc.tissue(3).ngaus = 2;
matlabbatch{2}.spm.spatial.preproc.tissue(3).native = [1 0];
matlabbatch{2}.spm.spatial.preproc.tissue(3).warped = [0 1];
matlabbatch{2}.spm.spatial.preproc.tissue(4).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,4'};
matlabbatch{2}.spm.spatial.preproc.tissue(4).ngaus = 3;
matlabbatch{2}.spm.spatial.preproc.tissue(4).native = [1 0];
matlabbatch{2}.spm.spatial.preproc.tissue(4).warped = [0 0];
matlabbatch{2}.spm.spatial.preproc.tissue(5).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,5'};
matlabbatch{2}.spm.spatial.preproc.tissue(5).ngaus = 4;
matlabbatch{2}.spm.spatial.preproc.tissue(5).native = [1 0];
matlabbatch{2}.spm.spatial.preproc.tissue(5).warped = [0 0];
matlabbatch{2}.spm.spatial.preproc.tissue(6).tpm = {'C:\Users\kasperla\Documents\Code\spm12\tpm\TPM.nii,6'};
matlabbatch{2}.spm.spatial.preproc.tissue(6).ngaus = 2;
matlabbatch{2}.spm.spatial.preproc.tissue(6).native = [0 0];
matlabbatch{2}.spm.spatial.preproc.tissue(6).warped = [0 0];
matlabbatch{2}.spm.spatial.preproc.warp.mrf = 1;
matlabbatch{2}.spm.spatial.preproc.warp.cleanup = 1;
matlabbatch{2}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{2}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{2}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{2}.spm.spatial.preproc.warp.samp = 3;
matlabbatch{2}.spm.spatial.preproc.warp.write = [0 1];
matlabbatch{2}.spm.spatial.preproc.warp.vox = NaN;
matlabbatch{2}.spm.spatial.preproc.warp.bb = [NaN NaN NaN
                                              NaN NaN NaN];
matlabbatch{3}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));
matlabbatch{3}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));
matlabbatch{3}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70
                                                          78 76 85];
matlabbatch{3}.spm.spatial.normalise.write.woptions.vox = [1 1 1];
matlabbatch{3}.spm.spatial.normalise.write.woptions.interp = 4;
matlabbatch{3}.spm.spatial.normalise.write.woptions.prefix = 'w';
matlabbatch{4}.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{4}.spm.spatial.smooth.fwhm = [3 3 3];
matlabbatch{4}.spm.spatial.smooth.dtype = 0;
matlabbatch{4}.spm.spatial.smooth.im = 0;
matlabbatch{4}.spm.spatial.smooth.prefix = 's';