Hi Martin, Thank you for the feedback. Our version of FS 5.3 is the centos4 build (which works perfectly) so I downloaded the same when got a copy of dev (nightly build 05-11-16). However, I just tried the centos6 and the brainstem module now works smoothly (including mri_robust_register). There must be a difference between FS 5.3 centos4, dev centos4 and dev centos6 but I have no clue of what that could be or if it even matters. I thought you might like to know.
Best, Vincent. On 17.05.2016 19:27, Martin Reuter wrote: > Hi Vincent, > > I tried it on my machine and it works. No segfault and the registration looks > good. Is your dev version older? I don't specifically remember fixing > anything recently, but it may be best to download a more recent > robust_register binary? It could also be that something else is incompatible > on your system (e.g. different centos versions etc). > > Best, Martin > > On 05/13/2016 10:29 AM, Vincent Beliveau wrote: > > Hi Martin, > > I assume you want the actual inputs, not the command, sorry about that ;) > I've attached the tmp folder created by the brainstem module. > > Best, > > Vincent. > > On 13.05.2016 16:21, Vincent Beliveau wrote: > > 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 [1] > www.bcbl.eu [2] > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer [3] > > ------------------------- > > 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > 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. > > -- > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > 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. -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- 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 Links: ------ [1] http://www.jeiglesias.com [2] http://www.bcbl.eu [3] http://www.bcbl.eu/legal-disclaimer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
