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Loop in SPM batch not working

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Elizabeth Matsiyevskiy
Elizabeth Matsiyevskiy on 13 Dec 2019
Edited: Cris LaPierre on 18 Mar 2020
For some reason when I try passing the subjects into the subjMP path, the subject isn't inserted into the path. Is there another way I should script it to get into each subjects directory? When I run the code line by line this is the output I get for the subjects:
'ifs/loni/faculty/mbraskie/HABLE/MPRAGE/὞/baseline/*_MPRAGE.nii.gz'
%% MATLAB AND SPM12 BATCH SCRIPTING:
% Processing segmentation single-subject T1 for PET roi analysis
% Testing
SPM12='/usr/local/spm12';
AAL3='/ifs/loni/faculty/mbraskie/HABLE/PET/spmtest/AAL3';
MPRAGE='/ifs/loni/faculty/mbraskie/HABLE/MPRAGE';
addpath (genpath(SPM12));
addpath (genpath(AAL3));
addpath (genpath(MPRAGE));
targets = [8030 8483];
for subj = targets
subjMP=fullfile(MPRAGE,subj,'baseline','*_MPRAGE.nii.gz')
cd (subjMP); mkdir spm; cd spm;
spm;
matlabbatch{1}.spm.spatial.preproc.channel.vols = {'${subjMP},1'};
matlabbatch{1}.spm.spatial.preproc.channel.biasreg = 0.001;
matlabbatch{1}.spm.spatial.preproc.channel.biasfwhm = 60;
matlabbatch{1}.spm.spatial.preproc.channel.write = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(1).tpm = {'/usr/local/spm12/tpm/TPM.nii,1'};
matlabbatch{1}.spm.spatial.preproc.tissue(1).ngaus = 1;
matlabbatch{1}.spm.spatial.preproc.tissue(1).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(1).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(2).tpm = {'/usr/local/spm12/tpm/TPM.nii,2'};
matlabbatch{1}.spm.spatial.preproc.tissue(2).ngaus = 1;
matlabbatch{1}.spm.spatial.preproc.tissue(2).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(2).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(3).tpm = {'/usr/local/spm12/tpm/TPM.nii,3'};
matlabbatch{1}.spm.spatial.preproc.tissue(3).ngaus = 2;
matlabbatch{1}.spm.spatial.preproc.tissue(3).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(3).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(4).tpm = {'/usr/local/spm12/tpm/TPM.nii,4'};
matlabbatch{1}.spm.spatial.preproc.tissue(4).ngaus = 3;
matlabbatch{1}.spm.spatial.preproc.tissue(4).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(4).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(5).tpm = {'/usr/local/spm12/tpm/TPM.nii,5'};
matlabbatch{1}.spm.spatial.preproc.tissue(5).ngaus = 4;
matlabbatch{1}.spm.spatial.preproc.tissue(5).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(5).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(6).tpm = {'/usr/local/spm12/tpm/TPM.nii,6'};
matlabbatch{1}.spm.spatial.preproc.tissue(6).ngaus = 2;
matlabbatch{1}.spm.spatial.preproc.tissue(6).native = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(6).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.warp.mrf = 1;
matlabbatch{1}.spm.spatial.preproc.warp.cleanup = 1;
matlabbatch{1}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{1}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{1}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{1}.spm.spatial.preproc.warp.samp = 3;
matlabbatch{1}.spm.spatial.preproc.warp.write = [1 1];
end

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Answers (1)

Cris LaPierre
Cris LaPierre on 18 Mar 2020
Edited: Cris LaPierre on 18 Mar 2020
The issue I see is that you are trying to combine text and numbers using a function that is expecting all text. As you've observerd, that doesn't work:
'\ifs\loni\faculty\mbraskie\HABLE\MPRAGE\὞\baseline\*_MPRAGE.nii.gz'
Try first converting subj to text using num2str.
subjMP=fullfile(MPRAGE,num2str(subj),'baseline','*_MPRAGE.nii.gz')
'\ifs\loni\faculty\mbraskie\HABLE\MPRAGE\8030\baseline\*_MPRAGE.nii.gz'

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