Freesurfer

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30088 discussions

error during mri_cvs_register
by David Brang 21 Jun '11

21 Jun '11

Hi All I'm receiving an error with mri_cvs_register from FS 5.1 on a 64-bit Mac 10.6.7 system and was hoping for some help. It's the same error with the 3 subjects I've tried it on, and occurs both before and after using the mri_cvs_register that was updated on Jun 10th. I'm including the last few lines of the log file. Thanks David ---------LOG---------- step = 12 =============== elt_vol= 15.0625 Constructing Delaunay tetrahedralization. Delaunay seconds: 7.9e-05 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0.000686 Removing unwanted tetrahedra. Hole seconds: 3.3e-05 Repairing mesh. Repair seconds: 6.9e-05 Adding Steiner points to enforce quality. Quality seconds: 4.27942 Smoothing mesh. Smooth seconds: 0.299788 Writing nodes. Writing elements. Writing faces. Output seconds: 0.036639 Total running seconds: 4.61682 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 81870 Mesh tetrahedra: 491585 Mesh faces: 995562 Mesh subfaces: 24784 Mesh subsegments: 530 Saving nodes to iteration.node Saving elements to iteration.ele Saving faces to iteration.face mesh nodes = 81870 mesh elts = 491585 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.302 seconds element count = 1128168 count inserted = 200000 elapsed = 0.496 seconds element count = 3256402 count inserted = 300000 elapsed = 0.411 seconds element count = 5222879 count inserted = 400000 elapsed = 0.343 seconds element count = 7039018 done building octree - total elements = 8705605 penalty_weight = 1000 setting bc 205.891 174.948 225.515 -> 0 0 0 instead 205.881 174.938 225.505 -> norm = 0.0173205 setting bc 205.891 174.948 27.6148 -> 0 0 0 instead 205.881 174.938 27.6248 -> norm = 0.0173205 setting bc 205.891 35.1985 225.515 -> 0 0 0 instead 205.881 35.2085 225.505 -> norm = 0.0173205 setting bc 205.891 35.1985 27.6148 -> 0 0 0 instead 205.881 35.2085 27.6248 -> norm = 0.0173205 setting bc 52.3002 174.948 225.515 -> 0 0 0 instead 52.3102 174.938 225.505 -> norm = 0.0173205 setting bc 52.3002 174.948 27.6148 -> 0 0 0 instead 52.3102 174.938 27.6248 -> norm = 0.0173205 setting bc 52.3002 35.1985 225.515 -> 0 0 0 instead 52.3102 35.2085 225.505 -> norm = 0.0173205 setting bc 52.3002 35.1985 27.6148 -> 0 0 0 instead 52.3102 35.2085 27.6248 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 92200 Total BCs = 548640 no-eqs = 245610 surf2vol(4634) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [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 0 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 295714444! [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 darwin9.8 named Psytechs-Mac-Pro.local by dbrang Fri Jun 17 17:23:37 2011 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [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 10 BUS: Bus Error, possibly illegal memory access [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…: 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 darwin9.8 named Psytechs-Mac-Pro.local by dbrang Fri Jun 17 17:23:37 2011 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [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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launchpad help
by Chindhuri Selvadurai 21 Jun '11

21 Jun '11

Hello, I am trying to do recon-all using launchpad, and I am not sure how to fix the error I am getting. I checked IT's launchpad help website, but can't seem to figure it out. Using fs v4 subjects_dir: /space/ventzl/36/users/RespMon12C/subjects command: pbsubmit -q sergeant -l nodes=1:opteron -m chinsel -c 'recon-all -s RMAUT021 -all -i /cluster/archive/292/siemens/TrioTim-35006-20110508-105030-353000/353000-000004-000001.dcm -mail chinsel(a)nmr.mgh.harvard.edu -force' This is the output I'm getting: Opening pbsjob_3 qsub -V -S /bin/sh -m abe -M chinsel -q sergeant -l nodes=1:opteron -r n /pbs/chinsel/pbsjob_3 qsub: Unknown queue MSG=cannot locate queue FATAL: qsub call failed. Check above for error messages. I'm also not getting any e-mails. Is there a way to check an error log like on seychelles? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307

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trouble with longitudinal processing in FS5.1
by Jane Lawrence 21 Jun '11

21 Jun '11

Hello FreeSurfer community, I am running into a problem with my longitudinal data in the new FS5.1 and am wondering if anyone else has run into this error message during the unbiased template creation. I have 4 scans from 2 subjects and have run into the same error at the same place. I only run into this problem when I try running the analysis on all 4 scans - it has completed without error whenever I have tried different combinations of 2 or 3 scans so I don't think it is a problem with my data. The unbiased template creation gets to the point of Registration:computeMultiresRegistration and completes TP 1 and 2. When it gets to TP 3, it runs fine until it starts calculating Resolution: 0 S(256 256 256 ) T (256 256 256) On Iteration(f):2 I get the message "Killed". Since there isn't much info in the error message I'm having trouble figuring out what to troubleshoot next. As I mentioned above, I get this error message in 2 subjects in exactly the same place and the process completes without error when I use separate combinations so I don't think it's a data problem. And since 3 time points have run successfully I don't think that it is an issue of not having enough computer resources..... I am running freesurfer in a Oracle virtual box on a windows 64 bit computer. Any suggestions would be greatly appreciated. Cheers, Jane Lawrence Postdoctoral Fellow Perception and Action Laboratory Department of Psychology University of Manitoba

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recon-all exicted with ERROR
by Antonella Kis 21 Jun '11

21 Jun '11

Dear All, I just installed my new FS version (I saved my old version under freesurfer_backup). I am getting an error when I am running recon-all on my GNU/LINUX.Do I need a license file before running? What steps I need to follow before running the new FS version? Here is the outcome: [elysa@EW-LNX2 _orig_]# su [root@EW-LNX2 _orig_]# tcsh [elysa@EW-LNX2 _orig_]# setenv FREESURFER_HOME /usr/local/freesurfer/ [elysa@EW-LNX2 _orig_]# setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/june2011/_orig_/ [elysa@EW-LNX2 _orig_]# cd june2011 june2011: No such file or directory. [elysa@EW-LNX2 _orig_]# recon-all -s NPI001 -i /usr/local/freesurfer/subjects/june2011/_orig_/NPI001.nii.gz -qcache -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/june2011/_orig_ Actual FREESURFER_HOME /usr/local/freesurfer Linux EW-LNX2 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:54:20 EST 2010 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/june2011/_orig_/NPI001 mri_convert /usr/local/freesurfer/subjects/june2011/_orig_/NPI001.nii.gz /usr/local/freesurfer/subjects/june2011/_orig_/NPI001/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/june2011/_orig_/NPI001.nii.gz /usr/local/freesurfer/subjects/june2011/_orig_/NPI001/mri/orig/001.mgz -------------------------------------------------------------------------- ERROR: FreeSurfer license file /usr/local/freesurfer//.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /usr/local/freesurfer/subjects/june2011/_orig_/NPI001.nii.gz... Linux EW-LNX2 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:54:20 EST 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s NPI001 exited with ERRORS at Tue Jun 21 11:21:55 EDT 2011 For more details, see the log file /usr/local/freesurfer/subjects/june2011/_orig_/NPI001/scripts/recon-all.log THANK YOU! Antonella

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new version of qdec
by Jeanette Berberich 20 Jun '11

20 Jun '11

Hey All, Is there anywhere I can download just the newest version of the qdec files ($FREESURFER_HOME/bin/: qdec, qdec_glmfit and qdec.bin)? I want the abilities of the newer qdec but want to keep the version of freesurfer I have to keep my current data consistent. Thank you, Jeanette

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Uninstall FS
by Antonella Kis 20 Jun '11

20 Jun '11

Hello Experts, I apologise for the stupidity of this question, but I am not used to using Linux, but I need to uninstall my Freesurfer from the Desktop and then reinstall it,however, I have no idea how to uninstall in Linux. I was trying to execute: rm -rf /desktop/freesurfer but is not doing anything. Can someone possibly assist me in this problem? Id be extremely grateful. Thank you and Kind regards, Antonella

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display error
by Cris Lanting 20 Jun '11

20 Jun '11

Dear Freesurfer community, I have a display problem that affects especially tkmedit and tksurfer. We run freesurfer ( freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) on a remote unix server and use Exceed (v. 14.0.0.376) to port the display to a local (windows) computer. At first we got a openGL error stating that OpenGL was not supported when calling e.g. tksurfer. Now we have installed Exceed 3D to support OpenGL it seems to continue beyond the previous error message but comes up with a different one (see snippet) <snippet> subject is js hemi is rh surface is pial surfer: current subjects dir: /home/cris/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/cris Reading image info (/home/cris/freesurfer/subjects/js) Reading /home/cris/freesurfer/subjects/js/mri/orig.mgz surfer: Reading header info from /home/cris/freesurfer/subjects/js/mri/orig.mgz fsurfer: vertices=156376, faces=312748 surfer: single buffered window surfer: tkoInitWindow(js) Window type not found! surfer: failed, trying double buffered window Window type not found! surfer: failed, no suitable display found <end snippet> Any ideas? Note that other programs that do not use OpenGL seem to run fine (i.e. fslview and gedit) Kind regards, Cris Lanting Career Development Fellow MRC Institute of Hearing Research Science Road, University Park Nottingham NG7 2RD cris(a)ihr.mrc.ac.uk

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Regarding Installation
by Antonella Kis 20 Jun '11

20 Jun '11

Hello, Can you please let me know how I can install on top of an old version the new version FreeSurfer v.5.1.0? Thank you. Antonella

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Regarding Installation
by Antonella Kis 20 Jun '11

20 Jun '11

Can you please let me know how I can install on top of an old version the new version FreeSurfer v.5.1.0? Thank you. Antonella -- ------------------------------ Dr.Antonella Kis, PhD Sessional Lecturer Life Sciences, Physics Department University of Toronto at Scarborough Clinical Research Project Coordinator The Hospital for Sick Children (SickKids) Diagnostic Imaging Department Neurosciences and Mental Health

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qdec roi analysis
by fabrizio piras 20 Jun '11

20 Jun '11

Dear all, I run a controls vs patients thickness analysis using qdec and got several results. Now, it is not entirely clear to me how to refine my surface-based analysis (still using qdec) into a ROI, the middle orbitofrontal region. Cheers, Fabrizio --------------------------- Fabrizio Piras Ph.D. --------------------------- Fondazione I.R.C.C.S. Santa Lucia Laboratorio di Neuropsichiatria via Ardeatina 306 tel +390651501547 fax +390651501213 Il giorno 18/giu/11, alle ore 18:00, freesurfer-request(a)nmr.mgh.harvard.edu ha scritto: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Automated QC of Freesurfer Images (West, John D.) > 2. [Fwd: Welcome to the "Freesurfer" mailing list (Digest mode)] > (Antonella Kis) > 3. Re: Automated QC of Freesurfer Images (Louis Nicholas Vinke) > 4. Re: Automated QC of Freesurfer Images (Douglas N Greve) > 5. Two timepoints - same subject, correlation matrix (Sudhin A. > Shah) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Jun 2011 20:11:55 +0000 > From: "West, John D." <jdwest(a)iupui.edu> > Subject: [Freesurfer] Automated QC of Freesurfer Images > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <793D43FE7976404CB5E172709AB1F4080DE8E659(a)IU-MSSG-MBX102.ads.iu.edu> > Content-Type: text/plain; charset="us-ascii" > > Hello. > > We are in the process of trying to develop a QC pipeline for our > Freesurfer processed images. I was wondering if anyone has > developed any type of automated QC they would be willing to share > with us or have any suggestions on how to proceed. > > Any help would be most appreciated. > > Thanks. > -John West > Systems Admin/Imaging Analyst > IU Center for Neuroimaging >

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