External Email - Use Caution
Dear,
I encountered the following error when I tried to run mri_gtmpvc -- rbv:
Segmentation fault (core dumped)
First I performed the PET to orig registration using spmregister, secondly I tried with the registration using mri_coreg but the error remained. I also redid the segmentation step gtmseg --s $word --xcerseg without fixing the problem. Can anyone help me with this problem?
The code I tried to run:
#mri_gtmpvc --i SUVR_cerebellum.nii.gz --reg suv.reg.lta --psf 5 --seg /gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8
Kind regards Donatienne
External Email - Use Caution
On March 13, 2019 at 9:18 PM Donatienne Van Weehaeghe donatienne.vanweehaeghe@uzleuven.be wrote: The code I tried to run:
#mri_gtmpvc --i SUVR_cerebellum.nii.gz --reg suv.reg.lta --psf 5 --seg /gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8
Is that slash in the part '--seg /gtmseg.mgz' a copy & paste error? If not: it is very likely that the file does not exist in that location.
I'm not sure though whether that is the cause of the error. I would rather expect a "file not found" error message instead of a seg fault in that case. But it's worth checking.
External Email - Use Caution
Dear,
Apologies, this is a copy and paste error the full command was:
#mri_gtmpvc --i /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$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/$word/PVC/gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8
Kind regards
Donatienne
________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu namens Tim Schäfer ts+ml@rcmd.org Verzonden: woensdag 13 maart 2019 23:22:07 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Segmentation fault
External Email - Use Caution
On March 13, 2019 at 9:18 PM Donatienne Van Weehaeghe donatienne.vanweehaeghe@uzleuven.be wrote: The code I tried to run:
#mri_gtmpvc --i SUVR_cerebellum.nii.gz --reg suv.reg.lta --psf 5 --seg /gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8
Is that slash in the part '--seg /gtmseg.mgz' a copy & paste error? If not: it is very likely that the file does not exist in that location.
I'm not sure though whether that is the cause of the error. I would rather expect a "file not found" error message instead of a seg fault in that case. But it's worth checking.
-- Tim
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Can you send the command line with out variables and the full terminal output?
On 3/14/19 8:48 AM, Donatienne Van Weehaeghe wrote:
External Email - Use Caution
Dear,
Apologies, this is a copy and paste error the full command was:
#mri_gtmpvc --i /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$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-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 External Email - Use Caution
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
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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu namens Greve, Douglas N.,Ph.D. DGREVE@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 CautionDear,
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 External Email - Use Caution
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
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
freesurfer@nmr.mgh.harvard.edu
-
Donatienne Van Weehaeghe -
Greve, Douglas N.,Ph.D. -
Tim Schäfer