Freesurfer December 2011

freesurfer@nmr.mgh.harvard.edu

98 participants
157 discussions

downsampling 4D volume
by ythomas 10 Jan '12

10 Jan '12

Hi, I am trying to downsample a 4D volume using mri_convert. However, it seems to be killing the 4 dimension. For example, if I do mri_convert -voxsize 4 4 4 tmp.mgz tmp444.mgz The original volume which is 256 x 256 x 256 x 120 becomes 64 x 64 x 64. Thanks, Thomas

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anterior temporal lobe problems
by Michael Harms 10 Jan '12

10 Jan '12

Hi guys, We have a sample of 150+ pediatric brains that we pumped through FS 5.1, and in an easy majority of them the white/pial surface accuracy in the anterior temporal lobe is poor. I know that this is an area where problems have frequently been reported. What is it about that area in particular that makes it difficult to get accurate surfaces? (Is the contrast and SNR in that area inherently worse?) And, short of a large time commitment of control point and wm.mgz editing, are there any flags/tweaks that we could attempt to fix the problem in a more automatic fashion? thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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GLM design question
by Martijn Steenwijk 09 Jan '12

09 Jan '12

Dear all, I'm relatively new with Freesurfer, but slowly getting more and more used to it's great possibilities. To be 'sure', I've a question about the design of a GLM. I want to compare CT in Healthy Controls vs Diseased, and control for age and sex. It appears to me that factors (eg sex) cannot be used as covariate/variable, which forces me to model them as a separate class although I'm not interested in sex differences. This brings me to the following FSGD file: # HcDis.fsgd GroupDescriptorFile 1 Title HcDis Class Hc_Male Class Hc_Female Class Dis_Male Class Dis_Female Variables Age Input subjid1 Hc_Male 35 Input subjid2 Dis_Female 30 .. Then the difference between Hc and Dis, corrected for age and sex is given by the contrast matrix #Hc-vs-Dis.mtx 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 Is this correct? Best, Martijn

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How to export non spatial normalization fMRI images?
by Long 09 Jan '12

09 Jan '12

Hi, I have run preproc-sess to analyze fMRI images. I'd like to analyze fMRI images in the individual space, but I found that the final output (i.e., fmcpr.up.sm4.fsaverage.lh.nii.gz) were already spatial normalized. So, How to just smooth fMRI images in surface space and export them as the co-registered fMRI images in volume space? I think it could start at "fmcpr.up.nii.gz"? Thank you in advance! Best, Xiangyu Long

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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.

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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

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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

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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 > >

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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/

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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

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Freesurfer December 2011