Freesurfer January 2012

freesurfer@nmr.mgh.harvard.edu

97 participants
171 discussions

What effect will it give if software is used to change flip angle on a dicom image? Can Freesurfer change flip angle?
by Knut J Bjuland 07 Jan '12

07 Jan '12

Hi I have problem with two dataset processed with different version of Freesurfer but with the same subject. I am able to import the data set proceed with Freesurfer 4.30 into Freesurfer 5.1. But there was used some proprietary programs at FS 430 data for motion correction and contrast enhancement before the dicom files was input into Freesurfer. These proprietary programs change the flip angle from 7 degrees to 401.07 degrees. I am able to replicate findings that survive FDR but I get quite different result for findings that do not survive FDR. My theory is that the proprietary programs change the dicom in such manner that it gives a new dicom files. Is this correct? I do not have access to these programs anymore. What effect will it give if software is used to change flip angle on a dicom image? Can I use Freesurfer to force the flip angle back to 7 degree? I converted the files from Freesurfer 4.30 to Freesurfer 5.1 using recon –make all –s {subject}. I am enclosing the mri_info of the first files in Freesurfer pipeline. The vox to ras and ras to voxel is also changed. What effect will this have? Knut J

2 1

SPGR gadolinium contrast
by Cat Chong 05 Jan '12

05 Jan '12

Hello Experts: Is is possible to run 3D SPGR's with contrast (gadolineum) through freesurfer? Also, in a separate dataset, we have 3D SPGR's that have unfortunately been compressed. Can they still be run? Thanks, catherine

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QDEC:/ problems with generating stats Data Tables
by Cat Chong 05 Jan '12

05 Jan '12

HI Experts: Using Qdec, I have tried to generate Stats Data Tables, but below is the error message I received. .I get this error message for all subjects but the aseg.stats files are there and seem ok... any ideas of what I am doing wrong? cheers, catherine asegstats2table --common-segs --meas volume --tablefile /5000_series/5000_series/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 5002_out 5003_out 5005_out 5006_out SUBJECTS_DIR : /5000_series/5000_series Parsing the .stats files ERROR: The stats file /5000_series/5000_series/5002_out/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats file

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Segmentation Problem
by Markus Savli 05 Jan '12

05 Jan '12

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Re: [Freesurfer] Freesurfer Courses
by Allison Player 04 Jan '12

04 Jan '12

Hi Cat, Anyone who is interested in receiving emails about upcoming FreeSurfer courses should sign up for the mailing list here: http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi Registration is not yet open but an announcement about when it will open will go out to that list. Allison On Wed, 4 Jan 2012, Cat Chong wrote: > Hi Allison, > that would be great, is there a website I can check to register? > Cat > > ____________________________________________________________________________ > From: Allison Player <astevens(a)nmr.mgh.harvard.edu> > To: Cat Chong <cavecreekcutter(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Wednesday, January 4, 2012 10:29 AM > Subject: Re: [Freesurfer] Freesurfer Courses > > Hi Catherine, > We hope to have a course in Boston in April. > Allison > > On Wed, 4 Jan 2012, Cat Chong wrote: > > > Hi all, > > > > Just checking.. is the Freesurfer course in New Zealand this May the only > > course offered this year, or are there others? > > would love to go.... but New Zealand may be a stretch... > > cheers, > > catherine > > > > > _______________________________________________ > > 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. > > > >

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Freesurfer Courses
by Cat Chong 04 Jan '12

04 Jan '12

Hi all, Just checking.. is the Freesurfer course in New Zealand this May the only course offered this year, or are there others? would love to go.... but New Zealand may be a stretch... cheers, catherine

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recon-all problem
by LAOUCHEDI MAKHLOUF 04 Jan '12

04 Jan '12

hi everyone thank you very much for your help; i've sent the link to the Administrator of the grid and wil have the answer tomorow thank you again

1 0

PETSC ERROR
by Antonella Kis 04 Jan '12

04 Jan '12

Hi, I got a PETSC ERROR while I was running the mri_cvs_register: mri_cvs_register --mov C12 --noaseg. I found online about this problem and I followed the solution that was posted online by updating my Cshell script for the mri_cvs_register but this does not fixed my problem and I am still getting the PETSC ERROR. I attached the log file to my email. I am using: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: CentOS release 5.7 (Final) Kernel info: Linux 2.6.18-274.12.1.el5 x86_64 And the ERROR mesage that I am getthing is: [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 Tue Jan 3 12:15:19 2012 [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 Tue Jan 3 12:15:19 2012 [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 I will apreciatte any help and/or suggestion. Thank you, Antonella Any help will be graetly appreciated.

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get_4dfp_dimoe problem
by LAOUCHEDI MAKHLOUF 04 Jan '12

04 Jan '12

hi everyone we run recon-all on a cloud and we obtained this error: mpr2mni305 failed, see transforms/talairach_avi.log The log says the file name is too long perhaps because of the tmp dir file names: get_4dfp_dimoe: /var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/https_3a_2f_2fwms01.ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-47e5-ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.img filename too long ERROR: 'imgreg_4dfp /var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/https_3a_2f_2fwms01.ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-47e5-ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/711-2C_as_mni_average_305 /var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/https_3a_2f_2fwms01.ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-47e5-ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/711-2B_as_mni_average_305_masktalsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=255 knowing that it is difficult for us to do things differently (to change the path); is it possible to do something in freesurfer to work with thesse filenames ? thanks for your help

3 3

follow up on question asked during freesurfer course
by Knut J Bjuland 04 Jan '12

04 Jan '12

Hi To compare data different version of Freesurfer I was advised to bring it into the same version, and the subjects are the same. I used recon-all –make –all –s to convert from Freesurfer 4.30 to Freesurfer 5.1. The results are now more similar but there are some differences for weak correlations. When I use mri_glmfit I get a different output fwhm with the two different dataset using Freesurfer 5.1. Would you recommend me to rerun the converted subject using recon-all –all? I usually get similar result on hemisphere and results that are more similar than before on the other hemisphere. I am enclosing two representative jpg files. I have used smoothing at fwhm 60 mm. Best regards Knut J Bjuland

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Freesurfer January 2012