Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Insula annotation on cortical surface
by Jie Shi 02 Jan '12

02 Jan '12

Hi, does anyone know whether the insula area has an annotation on the cortical surface segmented by FreeSurfer as isthmus, posterior cingulate, etc? Thanks a lot. Jie

2 1

FreeSurfer & Ubuntu 11.10
by James, Brian 31 Dec '11

31 Dec '11

Hi Everyone, I thought I would try installing FreeSurfer on Ubuntu because I was having so many issues trying to install Octave on CentOS. On the bright side, Ubuntu can download Octave directly from the repository. The downside is when I test my freesurfer install with tkmedit bert orig,mgz, I get the following error: /usr/local/freesurfer/tktools/tksurfer.bin: Exec format error. Binary file not executable. Is there is something additional I need to install because it is on Ubuntu? Brian James Technical Applications Analyst North Bay Regional Health Centre<http://www.nbrhc.on.ca/> (705) 474-8600 x2611 The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately. L'information contenue dans ce message ?lectronique est destin?e uniquement au destinataire ou aux destinataires vis?s. La transmission de ce message ? une personne autre que son destinataire ou ses destinataires vis?s ne supprime en rien l'obligation d'en respecter la confidentialit?. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient ?tre soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la sant?. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires vis?s sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer imm?diatement et en avertir l'exp?diteur.

4 6

Registration Error
by Antonella Kis 30 Dec '11

30 Dec '11

Hi, I have a problem with mri_cvs_register. I am getthing the following error and I will be very grateful if you can help me to fix it (I am don't understand what means this errors). Also, after running a group analysis with mri_glmfit-sim and using the option --grf (so I have the survining clusters after multiple comparison) what is the best way to do a comparison between two groups for my DTI data (more exactly I am interested in comparing the FA values)? Many thaks and Happy New Year! Antonella [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process -2147483648 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 779465992! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: surf2vol on a linux-gnu named EW-LNX2 by root Thu Dec 29 14:34:49 2011 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: MatCreateSeqAIJ() line 2703 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: TSolver::setup_matrix() line 658 in unknowndirectory/solver.h [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: surf2vol on a linux-gnu named EW-LNX2 by root Thu Dec 29 14:34:49 2011 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

2 1

recon all problem
by LAOUCHEDI MAKHLOUF 30 Dec '11

30 Dec '11

i looked in the .bashrc file and it is written : FREESURFER_HOME=/home/amesse/software/freesurfer5.1 ; but freesurfer is installed in another account to which i have no access for the moment. i'll see it on monday thank you michael

1 0

Re: [Freesurfer] aparc.a2009s+aseg problem
by Michael Harms 30 Dec '11

30 Dec '11

You said initially that you were using FS v5.1, but that recon- all.local-copy is not consistent with FS v5.1. Are you processing subjects from scratch? If so, then you need to check your path/environment and figure out why an older version of recon-all is being called when you think that you're using v5.1. Please cc the list on communication so that the thread is captured in the FS archives for others benefit. cheers, -MH On Fri, 2011-12-30 at 16:52 +0000, LAOUCHEDI MAKHLOUF wrote: > hi michael > in fact i gedited the recon-all.local-copy in > <subjdir>/scripts and i noticed that the section "Cortical > Parcellation 2 " contains references to a2005s and not to a2009s. is > it a good idea to replace a2005s by a2009s in the text, then make a > copy of the file and put it somewhere (my current directory for > example) and then use it instead of the one given in > <FREESURFER_HOME>/bin ?. then should i do the same modifications in > the other parts of the text (for example the section "AParc2ASeg " and > "Surface Anatomical Stats 2" ...) ?. > i attached the recon-all.local-copy > file. > > thanks for all > > --- En date de : Ven 30.12.11, Michael Harms <mharms(a)conte.wustl.edu> > a écrit : > > De: Michael Harms <mharms(a)conte.wustl.edu> > Objet: Re: [Freesurfer] aparc.a2009s+aseg problem > À: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Date: Vendredi 30 décembre 2011, 16h57 > > > For some reason the beginning section of the recon-all.log > that you sent > is missing (i.e,. the part containing the actual command that > you ran). > What was the exact recon-all command that you used? From the > log file, > only the very first mri_convert was performed. Was your > command perhaps > recon-all -i <input.nii> -s <subjname> > > If so, you need to include the -all flag to actually run all > the rest of > the recon-all stream. > > cheers, > -MH > > > On Fri, 2011-12-30 at 13:55 +0000, LAOUCHEDI MAKHLOUF wrote: > > Hi Michael > > i looked in and the file doesn't contain a > section > > called "Cortical Parc 2" . what do you think is the > problem ? i > > attached the log > > > > thanks > > > > > > > > --- En date de : Jeu 29.12.11, Michael Harms > <mharms(a)conte.wustl.edu> > > a écrit : > > > > De: Michael Harms <mharms(a)conte.wustl.edu> > > Objet: Re: [Freesurfer] aparc.a2009s+aseg problem > > À: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr> > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Date: Jeudi 29 décembre 2011, 18h17 > > > > > > That is a job log from your cluster, which isn't > helpful to > > the issue at > > hand. > > > > You need to look in <subjdir>/scripts/recon-all.log, > which > > contains a > > complete log of the entire recon-all processing > stream. > > > > cheers, > > -MH > > > > On Thu, 2011-12-29 at 17:10 +0000, LAOUCHEDI > MAKHLOUF wrote: > > > Hi Michael > > > i looked in the job.log file (i am > using a > > condor > > > cluster) that i attached, and there is no such > section! > > > > > > thanks > > > > > > --- En date de : Jeu 29.12.11, Michael Harms > > <mharms(a)conte.wustl.edu> > > > a écrit : > > > > > > De: Michael Harms <mharms(a)conte.wustl.edu> > > > Objet: Re: [Freesurfer] aparc.a2009s+aseg > problem > > > À: "LAOUCHEDI MAKHLOUF" > <laoumakhl(a)yahoo.fr> > > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > > Date: Jeudi 29 décembre 2011, 18h01 > > > > > > > > > The problem is apparently that the > > Xh.aparc.a2009s.annot > > > wasn't created. > > > > > > Look in scripts/recon-all.log and make > sure that the > > section > > > "Cortical > > > Parc 2" is present, and if it is, look for > clues as > > to why > > > the .annot > > > wasn't created. > > > > > > cheers, > > > -MH > > > > > > On Thu, 2011-12-29 at 16:03 +0000, > LAOUCHEDI > > MAKHLOUF wrote: > > > > hi everyone > > > > i run recon-all on 27 > subjects > > using the > > > 5.1 > > > > version, and i don't find aparc.a2009s > +aseg.mgz > > neither > > > > lh.aparc.a2009s.annot so i can't use the > command > > > mri_aparc2aseg > > > > ( mri_aparc2aseg --s subject --a2009s). > what must > > i do to > > > have > > > > aparc.a2009s+aseg.mgz. > > > > > > > > thanks > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)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. > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

1 0

fixing hemisphere leakage
by David Groppe 30 Dec '11

30 Dec '11

Hi FreeSurfers, I'm trying to fix FreeSurfer's pial and white matter surface boundary estimates on a brain missing a large part of the right hemisphere. I've manually filled in the greatly expanded ventricles in the damaged hemisphere as white matter (see attached) and tried rerunning recon-all with -autorecon2-wm and -autorecon3 flags. This fails to help. Is there sometime else I can do? thanks in advance, -David -- David Groppe, Ph.D. Postdoctoral Researcher North Shore LIJ Health System New Hyde Park, New York http://www.cogsci.ucsd.edu/~dgroppe/

3 4

recon all problem
by LAOUCHEDI MAKHLOUF 30 Dec '11

30 Dec '11

hi michael in fact i gedited the recon-all.local-copy in <subjdir>/scripts and i noticed that the section "Cortical Parcellation 2 " contains references to a2005s and not to a2009s. is it a good idea to replace a2005s by a2009s in the text, then make a copy of the file and put it somewhere (my current directory for example) and then use it instead of the one given in <FREESURFER_HOME>/bin ?. then should i do the same modifications in the other parts of the text (for example the section "AParc2ASeg " and "Surface Anatomical Stats 2" ...) ?. i attached the recon-all.local-copy file. thanks for all

1 0

Re: [Freesurfer] aparc.a2009s+aseg problem
by Michael Harms 30 Dec '11

30 Dec '11

For some reason the beginning section of the recon-all.log that you sent is missing (i.e,. the part containing the actual command that you ran). What was the exact recon-all command that you used? From the log file, only the very first mri_convert was performed. Was your command perhaps recon-all -i <input.nii> -s <subjname> If so, you need to include the -all flag to actually run all the rest of the recon-all stream. cheers, -MH On Fri, 2011-12-30 at 13:55 +0000, LAOUCHEDI MAKHLOUF wrote: > Hi Michael > i looked in and the file doesn't contain a section > called "Cortical Parc 2" . what do you think is the problem ? i > attached the log > > thanks > > > > --- En date de : Jeu 29.12.11, Michael Harms <mharms(a)conte.wustl.edu> > a écrit : > > De: Michael Harms <mharms(a)conte.wustl.edu> > Objet: Re: [Freesurfer] aparc.a2009s+aseg problem > À: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Date: Jeudi 29 décembre 2011, 18h17 > > > That is a job log from your cluster, which isn't helpful to > the issue at > hand. > > You need to look in <subjdir>/scripts/recon-all.log, which > contains a > complete log of the entire recon-all processing stream. > > cheers, > -MH > > On Thu, 2011-12-29 at 17:10 +0000, LAOUCHEDI MAKHLOUF wrote: > > Hi Michael > > i looked in the job.log file (i am using a > condor > > cluster) that i attached, and there is no such section! > > > > thanks > > > > --- En date de : Jeu 29.12.11, Michael Harms > <mharms(a)conte.wustl.edu> > > a écrit : > > > > De: Michael Harms <mharms(a)conte.wustl.edu> > > Objet: Re: [Freesurfer] aparc.a2009s+aseg problem > > À: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr> > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Date: Jeudi 29 décembre 2011, 18h01 > > > > > > The problem is apparently that the > Xh.aparc.a2009s.annot > > wasn't created. > > > > Look in scripts/recon-all.log and make sure that the > section > > "Cortical > > Parc 2" is present, and if it is, look for clues as > to why > > the .annot > > wasn't created. > > > > cheers, > > -MH > > > > On Thu, 2011-12-29 at 16:03 +0000, LAOUCHEDI > MAKHLOUF wrote: > > > hi everyone > > > i run recon-all on 27 subjects > using the > > 5.1 > > > version, and i don't find aparc.a2009s+aseg.mgz > neither > > > lh.aparc.a2009s.annot so i can't use the command > > mri_aparc2aseg > > > ( mri_aparc2aseg --s subject --a2009s). what must > i do to > > have > > > aparc.a2009s+aseg.mgz. > > > > > > thanks > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)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. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

wm edit freeview
by Sabin Khadka 29 Dec '11

29 Dec '11

Dear all, Is there any documentation on doing em edit using freeview. Thanks, SK

2 1

Re: [Freesurfer] aparc.a2009s+aseg problem
by Michael Harms 29 Dec '11

29 Dec '11

That is a job log from your cluster, which isn't helpful to the issue at hand. You need to look in <subjdir>/scripts/recon-all.log, which contains a complete log of the entire recon-all processing stream. cheers, -MH On Thu, 2011-12-29 at 17:10 +0000, LAOUCHEDI MAKHLOUF wrote: > Hi Michael > i looked in the job.log file (i am using a condor > cluster) that i attached, and there is no such section! > > thanks > > --- En date de : Jeu 29.12.11, Michael Harms <mharms(a)conte.wustl.edu> > a écrit : > > De: Michael Harms <mharms(a)conte.wustl.edu> > Objet: Re: [Freesurfer] aparc.a2009s+aseg problem > À: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Date: Jeudi 29 décembre 2011, 18h01 > > > The problem is apparently that the Xh.aparc.a2009s.annot > wasn't created. > > Look in scripts/recon-all.log and make sure that the section > "Cortical > Parc 2" is present, and if it is, look for clues as to why > the .annot > wasn't created. > > cheers, > -MH > > On Thu, 2011-12-29 at 16:03 +0000, LAOUCHEDI MAKHLOUF wrote: > > hi everyone > > i run recon-all on 27 subjects using the > 5.1 > > version, and i don't find aparc.a2009s+aseg.mgz neither > > lh.aparc.a2009s.annot so i can't use the command > mri_aparc2aseg > > ( mri_aparc2aseg --s subject --a2009s). what must i do to > have > > aparc.a2009s+aseg.mgz. > > > > thanks > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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