External Email - Use Caution We just found the mistake. I created the SUVR images already in T1 space so I remade the lta files using the SUVR images and now it works.
Kind regards Donatienne ________________________________ Van: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> namens Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> Verzonden: donderdag 14 maart 2019 17:17:54 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Segmentation fault Can you send the command line with out variables and the full terminal output? On 3/14/19 8:48 AM, Donatienne Van Weehaeghe wrote: > > External Email - Use Caution > > 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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> namens Tim Schäfer > <ts...@rcmd.org> > *Verzonden:* woensdag 13 maart 2019 23:22:07 > *Aan:* Freesurfer support list > *Onderwerp:* Re: [Freesurfer] Segmentation fault > External Email - Use Caution > > > On March 13, 2019 at 9:18 PM Donatienne Van Weehaeghe > <donatienne.vanweehae...@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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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