Hi Eugenio and Vincent,
I cannot remember when I say robust_register crash the last time. It
should never happen. So it could also be that the inputs are already
corrupted. Can you send the inputs to that command so that I can try to
replicate and see if this is still a bug or what is going on?
Thanks, Martin
On 05/13/2016 09:54 AM, Eugenio Iglesias wrote:
It seems that mri_robust_register crashed. Martin, any ideas?
The algorithm worked because the rough registration from the previous
step was apparently enough to yield a decent segmentation.
Maybe we should consider stopping the whole process if
mri_robust_register dies...
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
------------------------------------------------------------------------
*From: *"Vincent Beliveau" <vincent.beliv...@nru.dk>
*To: *"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
*Sent: *Friday, May 13, 2016 2:40:11 PM
*Subject: *[Freesurfer] segfault using brainstem module from dev version
Hi list (and Eugenio),
I've ran the brainstem module from the dev version on some data
processed with FS v5.3. The module created some great segmentations of
brainstem but when taking a closer look at the log file, there is 2
seg faults which occur when calls to mri_robust_register are made,
with the following output (full log attached, see line 319 and 371):
/data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register:
line 3: 36835 Segmentation fault mri_robust_register.bin "$@"
/data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register
--mov imageDump.mgz --dst
/indirect/data1/vbeliveau/atlas/proc/MR/recon_final/f5249_GD/tmp/BS_T1based//BS-DE-binaryMask_autoCropped.mgz
-lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50:
Segmentation fault
mv: cannot stat ?imageDump_coregistered.mgz?: No such file or directory
I'm curious about how is this affecting the overall process, as
otherwise everything appears to be working smoothly.
Best,
Vincent.
--
Vincent Beliveau, MSc
Neurobiology Research Unit
Juliane Maries Vej 28, 3rd floor
Rigshospitalet, building 6931
DK-2100 Copenhagen, Denmark
phone: +45 3545 6718
e-mail: vincent.beliv...@nru.dk <mailto:vincent.beliv...@nru.dk>
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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : http://reuter.mit.edu
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contains patient information, please contact the Partners Compliance HelpLine at
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