mris_register segmentation fault while running recon-all with -cm option on a scan with .6mm isotropic voxels
External Email - Use Caution
Hello FreeSurfer Developers,
I am trying to run the hippocampal and amygdala subfield segmentation and take advantage of the .6mm resolution of the scan. I was able to run recon-all successfully on the scan without the -cm option.
I get the following error:
------------------------------
SUBJECT nomove_xpace_06mm_tr3bcm
DATE Fri Aug 3 11:58:33 EDT 2018
USER flalonde
HOST cn0638
PROCESSOR x86_64
OS Linux
Linux cn0638 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $
/data/flalonde/freesurfer_dev/bin/recon-all
PWD /gpfs/gsfs4/users/CPB/3TD/6mm/subjects/nomove_xpace_06mm_tr3bcm/scripts
CMD mris_register -curv -rusage /gpfs/gsfs4/users/CPB/3TD/6mm/subjects/nomove_xpace_06mm_tr3bcm/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /data/flalonde/freesurfer_dev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg
I’ve attached a copy of the recon-all.log
1) Freesurfer version: freesurfer-linux-centos7_x86_64-dev-20180723-7bf4760
2) Platform: CentOS Linux release 7.5.1804 (Core)
3) uname -a: Linux felix.nimh.nih.gov 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached
The list mentions running a post-hoc surface deformation (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47309.html) using mris_make_surfaces as a workaround but I’m not sure if this is applies in my case or what the full command might be (e.g. mris_make_surfaces subjectname lh).
Thanks,
François M. Lalonde, Ph.D. DNU / HGB / DIRP / NIMH 10 Center Drive, Room 4N244 Bethesda, MD 20892-1600
Hi Francois, this is an mris_register bug from last month that should be fixed in the most recent dev distribution.
best, Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Lalonde, Francois (NIH/NIMH) [E]" flalonde@mail.nih.gov Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Tuesday, August 7, 2018 at 2:33 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mris_register segmentation fault while running recon-all with -cm option on a scan with .6mm isotropic voxels
External Email - Use Caution Hello FreeSurfer Developers,
I am trying to run the hippocampal and amygdala subfield segmentation and take advantage of the .6mm resolution of the scan. I was able to run recon-all successfully on the scan without the -cm option.
I get the following error:
------------------------------
SUBJECT nomove_xpace_06mm_tr3bcm
DATE Fri Aug 3 11:58:33 EDT 2018
USER flalonde
HOST cn0638
PROCESSOR x86_64
OS Linux
Linux cn0638 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $
/data/flalonde/freesurfer_dev/bin/recon-all
PWD /gpfs/gsfs4/users/CPB/3TD/6mm/subjects/nomove_xpace_06mm_tr3bcm/scripts
CMD mris_register -curv -rusage /gpfs/gsfs4/users/CPB/3TD/6mm/subjects/nomove_xpace_06mm_tr3bcm/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /data/flalonde/freesurfer_dev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg
I’ve attached a copy of the recon-all.log
1) Freesurfer version: freesurfer-linux-centos7_x86_64-dev-20180723-7bf4760
2) Platform: CentOS Linux release 7.5.1804 (Core)
3) uname -a: Linux felix.nimh.nih.gov 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached
The list mentions running a post-hoc surface deformation (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47309.html) using mris_make_surfaces as a workaround but I’m not sure if this is applies in my case or what the full command might be (e.g. mris_make_surfaces subjectname lh).
Thanks,
François M. Lalonde, Ph.D. DNU / HGB / DIRP / NIMH 10 Center Drive, Room 4N244 Bethesda, MD 20892-1600
freesurfer@nmr.mgh.harvard.edu
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Hoopes, Andrew -
Lalonde, Francois (NIH/NIMH) [E]