That did the trick, Simon! Thank you very much!
Bw
Eugenio
Von meinem iPhone gesendet
> Am 17.07.2019 um 17:26 schrieb <[log in to unmask]> <[log in to unmask]>:
>
> It took me a while to work this out. Try putting these lines before your cat batch job
>
> %Set up the desired spm if necessary
> addpath('/applications/spm/spm12/')
> spm('defaults','PET');
> spm_jobman('initcfg');
>
> %Set CAT12 defaults
> cat_get_defaults('extopts.expertgui',1);
> cat_get_defaults('output.CSF.native',1);
> cat_get_defaults('output.CSF.mod',1);
>
> ...
> Your batch job from the gui here
> ...
>
> and this at the end of script
> spm_jobman('run',matlabbatch);
>
> But changing the defaults files as you suggest should work as well I guess so perhaps something else is wrong (above also outputs native map to be modulated)?
>
> Simon
>
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping) <[log in to unmask]> On Behalf Of Eugenio Abela
> Sent: 17 July 2019 15:03
> To: [log in to unmask]
> Subject: [SPM] CAT12: get CSF maps and suppress results image
>
> Hi Chistian and others
>
> I'm running CAT12 within a MATLAB batch job. The CAT12 part is preceded by fMRI preprocessing, and the anatomical data are coregistered to the fMRI before CAT12 segmentation. I want to achieve two things: get CAT12 to write CSF maps (mwp3*) and to not print any image.
>
> I tried setting these options in the matlabbatch directly, i.e.
>
> matlabbatch{5}.spm.tools.cat.estwrite.extopts.admin.print = 0; to suppress the figure
> matlabbatch{5}.spm.tools.cat.estwrite.output.CSF.mod = 1; To write modulated noramlised CSF maps
>
> That didn't work; I therefore tried to change the cat_defaults.m on my system, i.e.
>
> cat.extopts.print = 0;
> cat.output.CSF.mod = 1;
>
> Also, because I read somewhere on the list that another user had done this, I also set the field "expertgui" to 1:
>
> cat.extopts.expertgui = 1;
>
> Again, that didn't seem to change anything, i.e. the image still got printed, and I still did not obtain a CSF map.
>
>
> How can I make this work?
>
> Thank you very much!
>
> Eugenio
>
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