Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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.

1 0

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

1 0

iSurf Brainview now ported to Mac
by Pedro Paulo de Magalhães Oliveira Junior 03 Jan '12

03 Jan '12

Today Apple released in the Mac Store, for free, the version of iSurf BrainView for Mac. It's yet not as complete as the iPad and iPhone version but it has some nice features to help you or your students to learn neuroanatomy using FreeSurfer automated parcellation and subcortical segmentation. You can download it at: http://itunes.apple.com/us/app/isurf-brainview-desktop/id491367143?ls=1&mt=… As usual, suggestions are welcome. Happy 2012 for everyone. PPJ --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441

1 0

Re: [Freesurfer] get_4dfp_dimoe problem
by Bruce Fischl 03 Jan '12

03 Jan '12

Hi Avi just running recon-all I think. Is there an env variable you use to specify a tmp dir or something? thanks Bruce On Tue, 3 Jan 2012, Snyder, Avi wrote: > It looks like both the command (imgreg_4dfp) and argument > (.../711-2B_as_mni_average_305_mask.4dfp.img) fields are garbled. > Evidently, operating system paths have not been correctly set. > The 4dfp suite of tools is available and probably could be installed but > I'm not sure that is what is wanted. > I don't understand what LAOUCHEDI MAKHLOUF is trying to do. > > > AZS > ----------------------------------------------------- > On 1/3/12 10:40 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >> this is actually not part of FreeSurfer proper, but rather something that >> Avi Synder (ccd) was kind enough to contribute. Avi: can you comment? >> >> thanks >> Bruce >> On >> Tue, 3 Jan 2012, LAOUCHEDI MAKHLOUF wrote: >> >>> 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/htt >>> ps_3a_2f_2fwms01. >>> >>> ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-47e >>> 5- >>> >>> ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/71 >>> 1- >>> 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-5994-47e >>> 5- >>> >>> ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/71 >>> 1- >>> 2C_as_mni_average_305 >>> /var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.i >>> >>> e/https_3a_2f_2fwms01.ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/ >>> .t >>> >>> mp/8d3aa62d-5994-47e5-ba6d-031806ec9ffb/systemExecTask8201883777111446775 >>> /f >>> reesurfer/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 > > > >

1 0

Transformation Matrix from 3D Space to Flattened Surface
by warre295＠umn.edu 03 Jan '12

03 Jan '12

Hello gurus, Thank you in advance for any assistance. I have seen questions similar to this in the archives, but I believe this is a distinct problem. I apologize if this has been addressed previously. I am trying to obtain a retinotopic map, but for reasons of compatibility and future analysis I would like to keep as much of the work in MATLAB as is possible. To date, I have used FreeSurfer to generate a flattened cortical surface with great success. I would like to at this point exit the FreeSurfer world and perform the remaining analysis in MATLAB. What would be most ideal is if I could obtain a matrix which I can import into MATLAB and calculate a statistic for a point on the *flattened* cortical surface as a function of that statistic calculated for each voxel. This includes the phase information for a retinotopic map, but really I am looking for a solution to a more general problem. In other words, I need the matrix T in the equation... T*[Statistic from each voxel] = [Statistic for each point of Flattened Surface] where T describes how each point on the surface is derived from some set of voxels. I imagine this is an incredibly naive question, and that this would require a fair amount of work involving multiple transformations if it is even possible at all. I appreciate any and all advice. Best wishes, Scott Warren Graduate Student, Department of Neuroscience University of Minnesota

2 1

Destrieux atlas 2002
by Klein, Holger 03 Jan '12

03 Jan '12

Dear freesurfers, dear Mr. Destrieux, I have a question concerning the destrieux atlas 2002: I need a distinct label "G_temp_sup-G_temp_transv_and_interm_S" , which is only available in this atlas version. I tried using "?.atlas2002_simple.gcs", but this atlas does not output the requested label - but the labels of the default ?.aparc.annot. How can I get the mentioned label (with the original boundaries of this region). Would be glad about any help, THX Holger

2 1

Running mri_anatomical_stats on many subjects
by Klein, Holger 03 Jan '12

03 Jan '12

Dear Freesurfers, Is there a possibility to run mri_anatomical_stats on many subjects? Otherwise it would be quite time_consuming. Many thanks, Holger

2 1

Linear Regression Analysis - Significant Slope?
by Adam Nitenson 03 Jan '12

03 Jan '12

Hi Doug et al, *I think this email got lost in the cracks before the holidays, so I am reposting* We have been working on a linear regression-type analysis (see attached analysis.info for analysis and slopepar for a sample paradigm file) that involves task-related activation in a working memory test. For each participant, there are four conditions: 1, 3, 5, and 7 items that need to be remembered. The question that we would like to ask is: for each voxel, does the slope of activation (i.e., the slope of the best-fit line as you move from 1 to 3 to 5 to 7 items, as calculated separately for each subject) differ from zero? The second-level analysis would determine if there is a significant difference in activation-related slope between groups. Based on previous discussion, the way we have been doing this is to modify the paradigm file to create the following contrast: Condition 2: activation during working memory, but weighted by condition so the 1 item condition is weighted as 1, the 3 item condition as 3, etc. Condition 0: fixation The contrast is Condition 2 minus Condition 0. However, this method of weighting does not appear to answer the question about slope, but rather focuses on a weighted average. Consider the following scenario, involving 5 subjects (A through E): The SLOPE column is calculated using the slope function of the spreadsheet (i.e., slope of best fit line, using values of 1...3...5...7 for the x-axis, and, say, for subject A, the values of 2...4...6...8 for the y-axis). The WEIGHTED column is calculated in the way that I think FS-FAST is doing it, which is as follows: ((1 * 1 item activ. value) + (3 * 3 item activ. value) + (5 * 5 item activ. value) + (7 * 7 item activ. value))/4 The SLOPE and WEIGHTED values (regardless of their different scale) are not really comparable. For example, for Subject A, the SLOPE value is 1 and the WEIGHTED value is 58, while for Subject E, the SLOPE value is 1.1 and the WEIGHTED value is 28. So when looking at the paradigm file, take the lines 76.57 2 3.4 5 213.42 2 2.29 7 Does this mean that the activation at the first timepoint is accounted for 5-fold and the second timepoint 7-fold? If this is the case then this analysis may not best represent what we are looking for. Is there a way to modify the paradigm file so that the analysis can focus on slope of the best fit line as opposed to the weighted average? Thanks, Josh Forwarded from: Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer