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Dear,


Apologies, this is a copy and paste error the full command was:


#mri_gtmpvc --i /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUVR_cerebellum.nii.gz --reg /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/suv.reg.lta --psf 5 --seg /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/PVC/gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8

Kind regards

Donatienne


Van: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> namens Tim Schäfer <ts+ml@rcmd.org>
Verzonden: woensdag 13 maart 2019 23:22:07
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Segmentation fault
 
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> On March 13, 2019 at 9:18 PM Donatienne Van Weehaeghe <donatienne.vanweehaeghe@uzleuven.be> wrote:
> The code I tried to run:
>
> #mri_gtmpvc --i SUVR_cerebellum.nii.gz --reg suv.reg.lta --psf 5 --seg /gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8
>

Is that slash in the part '--seg /gtmseg.mgz' a copy & paste error? If not: it is very likely that the file does not exist in that location.

I'm not sure though whether that is the cause of the error. I would rather expect a "file not found" error message instead of a seg fault in that case. But it's worth checking.

--
Tim

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