Dear Rodrigo,
This is the FSL list.
We're not very good at SPM questions.
All the best,
Mark
On 26 Jan 2012, at 19:17, Rodrigo Perea wrote:
> Hello,
> I was wondering if you could help me with this issue. I created a .m file so I can run the following script (below) but sometimes it works and sometimes it give me the following error:
>
> ??? Undefined function or method 'cfg_util' for input arguments of type 'cell'.
> Error in ==> spm_jobman at 207
> cjob = cfg_util('initjob', mljob); Error in ==> Dartel_Step1_PereaReviewed at 123 spm_jobman('run',matlabbatch);
>
>
> I am running the file in a for loop so I want run it several times for several subjects but I just want to know why I get this error regarding spm_jobman('run',matlabbatch). I know it works so assigning the files is not a problem but sometimes i get the error above :S
> Thanks in advance,
> Rodrigo
>
>
>
> Here is my .m file:
>
> for i = 1:length(ARRAY WITH ALL IMAGES),
>
> %
> ref = [IMAGE-Timepoint1(i)]
> mov = [IMAGE-Timepoint2(i)]
> %
> c1 = ['c1' file1name '.nii']
> jac = ['jy_' file2name '.nii']
> change = ['GMchange_' file1name '.nii']
>
> matlabbatch{1}.spm.spatial.coreg.estimate.ref = {ref};
> matlabbatch{1}.spm.spatial.coreg.estimate.source = {mov};
> matlabbatch{1}.spm.spatial.coreg.estimate.other = {''};
> matlabbatch{1}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';
> matlabbatch{1}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];
> matlabbatch{1}.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{1}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];
>
> matlabbatch{2}.spm.tools.hdw.data.ref = {ref};
> matlabbatch{2}.spm.tools.hdw.data.mov = {mov};
> matlabbatch{2}.spm.tools.hdw.bias_opts.nits = 8;
> matlabbatch{2}.spm.tools.hdw.bias_opts.fwhm = 60;
> matlabbatch{2}.spm.tools.hdw.bias_opts.reg = 1e-006;
> matlabbatch{2}.spm.tools.hdw.bias_opts.lmreg = 1e-006;
> matlabbatch{2}.spm.tools.hdw.warp_opts.nits = 8;
> matlabbatch{2}.spm.tools.hdw.warp_opts.reg = 4;
>
> matlabbatch{3}.spm.tools.preproc8.channel.vols = {ref};
> matlabbatch{3}.spm.tools.preproc8.channel.biasreg = 0.0001;
> matlabbatch{3}.spm.tools.preproc8.channel.write = [0 0];
> matlabbatch{3}.spm.tools.preproc8.tissue(1).tpm = {'/usr/local/spm8/toolbox/Seg/TPM.nii,1'};
> matlabbatch{3}.spm.tools.preproc8.tissue(1).ngaus = 2;
> matlabbatch{3}.spm.tools.preproc8.tissue(1).native = [1 1];
> matlabbatch{3}.spm.tools.preproc8.tissue(1).warped = [0 0];
> matlabbatch{3}.spm.tools.preproc8.tissue(2).tpm = {'/usr/local/spm8/toolbox/Seg/TPM.nii,2'};
> matlabbatch{3}.spm.tools.preproc8.tissue(2).ngaus = 2;
> matlabbatch{3}.spm.tools.preproc8.tissue(2).native = [1 1];
> matlabbatch{3}.spm.tools.preproc8.tissue(2).warped = [0 0];
> matlabbatch{3}.spm.tools.preproc8.tissue(3).tpm = {'/usr/local/spm8/toolbox/Seg/TPM.nii,3'};
> matlabbatch{3}.spm.tools.preproc8.tissue(3).ngaus = 2;
> matlabbatch{3}.spm.tools.preproc8.tissue(3).native = [1 0];
> matlabbatch{3}.spm.tools.preproc8.tissue(3).warped = [0 0];
> matlabbatch{3}.spm.tools.preproc8.tissue(4).tpm = {'/usr/local/spm8/toolbox/Seg/TPM.nii,4'};
> matlabbatch{3}.spm.tools.preproc8.tissue(4).ngaus = 3;
> matlabbatch{3}.spm.tools.preproc8.tissue(4).native = [0 0];
> matlabbatch{3}.spm.tools.preproc8.tissue(4).warped = [0 0];
> matlabbatch{3}.spm.tools.preproc8.tissue(5).tpm = {'/usr/local/spm8/toolbox/Seg/TPM.nii,5'};
> matlabbatch{3}.spm.tools.preproc8.tissue(5).ngaus = 4;
> matlabbatch{3}.spm.tools.preproc8.tissue(5).native = [0 0];
> matlabbatch{3}.spm.tools.preproc8.tissue(5).warped = [0 0];
> matlabbatch{3}.spm.tools.preproc8.tissue(6).tpm = {'/usr/local/spm8/toolbox/Seg/TPM.nii,6'};
> matlabbatch{3}.spm.tools.preproc8.tissue(6).ngaus = 2;
> matlabbatch{3}.spm.tools.preproc8.tissue(6).native = [0 0];
> matlabbatch{3}.spm.tools.preproc8.tissue(6).warped = [0 0];
> matlabbatch{3}.spm.tools.preproc8.warp.reg = 4;
> matlabbatch{3}.spm.tools.preproc8.warp.affreg = 'mni';
> matlabbatch{3}.spm.tools.preproc8.warp.samp = 3;
> matlabbatch{3}.spm.tools.preproc8.warp.write = [0 0];
>
> matlabbatch{4}.spm.util.imcalc.input = {c1,jac};
> matlabbatch{4}.spm.util.imcalc.output = change;
> matlabbatch{4}.spm.util.imcalc.outdir = {''};
> matlabbatch{4}.spm.util.imcalc.expression = 'i1.*(i2-1)';
> matlabbatch{4}.spm.util.imcalc.options.dmtx = 0;
> matlabbatch{4}.spm.util.imcalc.options.mask = 0;
> matlabbatch{4}.spm.util.imcalc.options.interp = 1;
> matlabbatch{4}.spm.util.imcalc.options.dtype = 4;
>
> spm_jobman('run',matlabbatch);
> end %for i
>
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