Hi Martin,

Thanks for the help. From the brainstem-structures.log, mri_robust_register is called by the brainstem module as follow:

/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

Best,

Vincent

On 13.05.2016 16:13, Martin Reuter wrote:

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.beliveau@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.beliveau@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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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.