Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

PETSC ERROR
by David Brang 22 Jun '11

22 Jun '11

Hi I posted a couple days ago about a PETSC ERROR with while running mri_cvs_register but I seem to be having a more general problem. I'm receiving the same error on two 10.6.7 macs as well as on a Windows running virtualbox, both while processing my own subjects and FS5.1 bert. I'm using the command mri_cvs_register --mov bert --template cvs_avg35 and between step = 17 and step = 12 (break point is consistent within the individual but differs between individuals) I receive the same PETSC error (end of log appended below). In the VB I doubled the amount of memory allocated to the system and bert crashed as the same point in the process. Thanks in advance David step = 16 =============== elt_vol= 19.8125 Constructing Delaunay tetrahedralization. Delaunay seconds: 0 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 0 Removing unwanted tetrahedra. Hole seconds: 0 Repairing mesh. Repair seconds: 0 Adding Steiner points to enforce quality. Quality seconds: 6.32 Smoothing mesh. Smooth seconds: 0.41 Writing nodes. Writing elements. Writing faces. Output seconds: 0.03 Total running seconds: 6.76 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 62502 Mesh tetrahedra: 372867 Mesh faces: 755978 Mesh subfaces: 20488 Mesh subsegments: 465 Saving nodes to iteration.node Saving elements to iteration.ele Saving faces to iteration.face mesh nodes = 62502 mesh elts = 372867 building index src done building the list count inserted = 0 elapsed = 0 seconds element count = 1 count inserted = 100000 elapsed = 0.307 seconds element count = 1457735 count inserted = 200000 elapsed = 0.44 seconds element count = 3996981 count inserted = 300000 elapsed = 0.338 seconds element count = 6263194 done building octree - total elements = 7845082 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 = 83286 Total BCs = 548640 no-eqs = 187506 [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 1973583872 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 225757228! [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 FreeSurfer by virtualuser Tue Jun 21 12:18:59 2011 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-i386/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Mon Jun 16 12:09:46 2008 [0]PETSC ERROR: Configure options --with-debugging=0 --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…: 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 FreeSurfer by virtualuser Tue Jun 21 12:18:59 2011 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-i386/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Mon Jun 16 12:09:46 2008 [0]PETSC ERROR: Configure options --with-debugging=0 --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

3 2

Error running recon-all
by Antonella Kis 22 Jun '11

22 Jun '11

Dear experts of the Freesurfer, I am just learning freesurfer software and I was running recon-all for a subject in my directory. I can view the volumes and surfaces and I would be very grateful if you can list the next steps to be followed. Do I need to make a data correction(check my data) after running the recon-all by running the autorecon-all or the autorecon1 and autorecon2, etc? Any help will be greatly appreciate. Thank you.

2 1

find corresponding coordinates of verteces
by Oya, Hiroyuki (UI Health Care) 22 Jun '11

22 Jun '11

Dear all, Is it possible to find the coordinates (ras and MNI) of every vertex points on a surface in matlab? Thank you. Hiroyuki ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

1 0

Questions about the Freesurfer course
by Mu Xue 22 Jun '11

22 Jun '11

Hello, Sorry to bother you at this time. I got some questions about the freesurfer course. I checked the materials on the following webpage http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial It seems like we could get all the materials from that website since when I click all the links they will directly go to some other webpages or PPT files. They all contain a bunch of information pretty much the same with the lecture content according to the schedule on line. I'm just wondering if there is any new and crucial feature will be taught during the course. If the course do provide some,could you please list some so we could take a serious consideration. In the beginning,I try to email fslcourse(a)fmrib.ox.ac.uk which is the contact information of that course, but they told me I'd better ask the FreeSurfer folks about that and try the FreeSurfer mailing list. So I do as they said now. Your patience will be highly appreciated! Thank you! Best regards, Mu Xue

2 1

Re: [Freesurfer] launchpad help
by Chindhuri Selvadurai 22 Jun '11

22 Jun '11

I thought the default was p10, so I just used that to try again, however I'm still getting that error with no extra info in the log. what is the name of the queue, maybe that is my problem: command: pbsubmit -q p10 -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' output: Opening pbsjob_4 qsub -V -S /bin/sh -m abe -M chinsel -q p10 -l nodes=1:opteron -r n /pbs/chinsel/pbsjob_4 qsub: Job exceeds queue resource limits MSG=cannot locate feasible nodes FATAL: qsub call failed. Check above for error messages. [1] + Done gedit pbsjob_3 > What exact website page are you using for help on launchpad? launchpad has no > opteron nodes so you should not be specifying that resource. Its queue names > are also different than seychelles. There is no sergeant queue. Read: > https://www.nmr.mgh.harvard.edu/martinos/itgroup/launchpad.html > On Tue, 21 Jun 2011, Chindhuri Selvadurai wrote: >> 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 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > --------------------------------------------------------------- > Paul Raines email: raines at nmr.mgh.harvard.edu > MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging > 149 (2301) 13th Street Charlestown, MA 02129 USA Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307

2 1

transforms/talairach_with_skull.lta during autorecon1 and autorecon2 - is it a bug or a feature
by Michael Scheel 22 Jun '11

22 Jun '11

Dear Freesurfer experts, we are testing a grid computer infrastructure for running freesurfer analysis and are evaluating consistency and reliability of freesurfer results across platforms. Before we start our tests across platforms we conducted some freesurfer analysis on the same computer and had some unexpected results. Subsequent executions of the freesurfer pipeline ("New invocation of recon-all") on a certain subject - without any manual editing in between - give different results. We have invoked recon-all up to four times and all results are different. We tested in particular the aseg.stats results, where we found different volume estimations (up to 4%) depending on the number of processing loops. Intermediate results have also been found to be different The effect is reproducible, meaning the nth invocation of recon-all on the subject gives always the nth result. We suspect that the cause is (following the pipeline documentation: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) the twofold generation of "talairach_with_skull.lta", once in the autorecon-1 and a second time in the autorecon-2 phase: autorecon1: mri_em_register -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta autorecon2: mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta and it seems that the step in autorecon1 is skipped if the file "talairach_with_skull.lta" is already present. We were wondering if this behaviour is intended, so are the FreeSurfer results expected to improve with multiple invocations, even without manual intervention? Shall they converge after sufficient re-runs? Any help or comments are highly appreciated. Best, Michael

2 1

Two timepoints - same subject, correlation matrix
by Sudhin A. Shah 22 Jun '11

22 Jun '11

Hi, Can somebody please help me figure out how to correct this issue? 1 subject - 2 functional scans 1) run recon-all on subject anatomical. 2) process functional series (using AFNI/FSL) - each individually. 3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each individually) This works (I don't know why since I am not doing anything to register them to a common space). 4) I get a square matrix of 109 (n x n correlation matrix) in 1 timepoint and 112 in 2nd timepoint. I would like to get the exact same number so I can compare them! Of course I can manually adjust the rows/columns later, but I am not sure this is the smartest way to do this. Can I do all the steps in Freesurfer? Thank you, S

2 4

Volume-based stream: SupraTentorial Volume and Lesion-Mask
by Righart, Ruthger Dr. 22 Jun '11

22 Jun '11

Dear All, We are making Volume-based analyses and I have a few questions. 1. The SupraTentorial BrainVolume is indicated in the aseg.stats. I found an explanation on http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats about the SupraTentorial Vol., but checking the formula by summing up Cortex + CorticalWhiteMatter + SubCortGray I do not arrive at the exact value of SupraTentorial as indicated in the aseg.stats; for some of my subjects this value is higher, for some lower. What could cause these differences except from differences between voxel-based measures (i.e., SubCortGray) and surface-based measures? Is CSF and ventricle volume already subtracted from this value? Please see below copied the aseg.stats file for one subject: Cortex 448248.101786 + CorticalWhiteMatter 404368.03125 + SubCortGray 215645 = 1068261.13. This differs from the supratentorial value indicated in aseg.stats, which is 1218507.78. 2. Is it possible to exclude lesions from the volume-based measures by incorporating a self-defined lesion mask for each subject? If there are any lesions in structures, I would like to subtract lesion volume these structures that are listed in aseg.stats. Best Regards, Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany Ruthger.Righart(a)med.uni-muenchen.de # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /Applications/freesurfer/ASegStatsLUT.txt --subject 1008 # # SUBJECTS_DIR /Network/Xgrid/freesurfer_M0HL # subjectname 1008 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 225756.920309, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 222491.181478, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 448248.101786, mm^3 # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere cortical white matter volume, 198684.625000, mm^3 # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere cortical white matter volume, 205683.406250, mm^3 # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white matter volume, 404368.031250, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 215645.000000, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 663893.101786, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1218507.775726, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1882094.762769, mm^3 # SegVolFile mri/aseg.mgz # SegVolFileTimeStamp 2010/12/01 23:41:35 # ColorTable /Applications/freesurfer/ASegStatsLUT.txt # ColorTableTimeStamp 2010/08/15 20:35:08 # InVolFile mri/norm.mgz # InVolFileTimeStamp 2010/12/01 18:52:15 # InVolFrame 0 # PVVolFile mri/norm.mgz # PVVolFileTimeStamp 2010/12/01 18:52:15 # Excluding Cortical Gray and White Matter # ExcludeSegId 0 2 3 41 42 # VoxelVolume_mm3 1 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader StructName # TableCol 5 FieldName Structure Name # TableCol 5 Units NA # TableCol 6 ColHeader normMean # TableCol 6 FieldName Intensity normMean # TableCol 6 Units MR # TableCol 7 ColHeader normStdDev # TableCol 7 FieldName Itensity normStdDev # TableCol 7 Units MR # TableCol 8 ColHeader normMin # TableCol 8 FieldName Intensity normMin # TableCol 8 Units MR # TableCol 9 ColHeader normMax # TableCol 9 FieldName Intensity normMax # TableCol 9 Units MR # TableCol 10 ColHeader normRange # TableCol 10 FieldName Intensity normRange # TableCol 10 Units MR # NRows 45 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 4 44165 44165.0 Left-Lateral-Ventricle 19.7155 16.3746 0.0000 89.0000 89.0000 2 5 2806 2806.0 Left-Inf-Lat-Vent 38.3263 15.7951 0.0000 83.0000 83.0000 3 7 13657 13657.0 Left-Cerebellum-White-Matter 81.6728 7.8804 19.0000 104.0000 85.0000 4 8 58247 58247.0 Left-Cerebellum-Cortex 66.2938 9.3009 14.0000 102.0000 88.0000 5 10 7895 7895.0 Left-Thalamus-Proper 85.7346 10.2295 28.0000 119.0000 91.0000 6 11 7039 7039.0 Left-Caudate 76.7953 9.8187 43.0000 106.0000 63.0000 7 12 9318 9318.0 Left-Putamen 80.9289 7.7446 46.0000 105.0000 59.0000 8 13 1860 1860.0 Left-Pallidum 101.4026 7.2644 68.0000 125.0000 57.0000 9 14 3552 3552.0 3rd-Ventricle 32.3747 10.6085 7.0000 78.0000 71.0000 10 15 5173 5173.0 4th-Ventricle 26.7739 9.2009 5.0000 69.0000 64.0000 11 16 21267 21267.0 Brain-Stem 80.5809 11.2668 0.0000 112.0000 112.0000 12 17 4285 4285.0 Left-Hippocampus 71.2247 8.9495 37.0000 103.0000 66.0000 13 18 2061 2061.0 Left-Amygdala 70.0988 7.7635 46.0000 95.0000 49.0000 14 24 2125 2125.0 CSF 45.0837 14.0328 0.0000 91.0000 91.0000 15 26 353 353.0 Left-Accumbens-area 74.6694 8.4345 36.0000 97.0000 61.0000 16 28 3929 3929.0 Left-VentralDC 91.5580 11.5144 25.0000 138.0000 113.0000 17 30 80 80.0 Left-vessel 69.7313 10.6466 44.0000 93.0000 49.0000 18 31 3060 3060.0 Left-choroid-plexus 53.4769 14.2466 16.0000 97.0000 81.0000 19 43 41682 41682.0 Right-Lateral-Ventricle 20.2051 17.6097 0.0000 95.0000 95.0000 20 44 2696 2696.0 Right-Inf-Lat-Vent 35.8659 13.8272 5.0000 82.0000 77.0000 21 46 13037 13037.0 Right-Cerebellum-White-Matter 78.5698 7.4065 15.0000 101.0000 86.0000 22 47 63878 63878.0 Right-Cerebellum-Cortex 62.0222 8.9751 9.0000 114.0000 105.0000 23 49 8346 8346.0 Right-Thalamus-Proper 82.2752 10.6945 17.0000 117.0000 100.0000 24 50 6893 6893.0 Right-Caudate 77.8693 10.4023 40.0000 107.0000 67.0000 25 51 7934 7934.0 Right-Putamen 82.6062 7.5576 35.0000 109.0000 74.0000 26 52 1465 1465.0 Right-Pallidum 99.2448 8.3569 66.0000 125.0000 59.0000 27 53 4524 4524.0 Right-Hippocampus 69.3366 8.3325 41.0000 100.0000 59.0000 28 54 2064 2064.0 Right-Amygdala 70.9995 7.2951 46.0000 94.0000 48.0000 29 58 495 495.0 Right-Accumbens-area 82.1215 7.6559 53.0000 102.0000 49.0000 30 60 3792 3792.0 Right-VentralDC 91.5163 11.6881 35.0000 139.0000 104.0000 31 62 60 60.0 Right-vessel 67.9400 12.2748 43.0000 95.0000 52.0000 32 63 2811 2811.0 Right-choroid-plexus 54.0732 12.8437 11.0000 105.0000 94.0000 33 72 2 2.0 5th-Ventricle 53.6667 15.3080 36.0000 63.0000 27.0000 34 77 76464 76464.0 WM-hypointensities 77.3176 11.2567 3.0000 116.0000 113.0000 35 78 0 0.0 Left-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 36 79 0 0.0 Right-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 37 80 176 176.0 non-WM-hypointensities 67.8028 9.9931 39.0000 87.0000 48.0000 38 81 0 0.0 Left-non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 39 82 0 0.0 Right-non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 40 85 279 279.0 Optic-Chiasm 74.4070 19.3980 32.0000 121.0000 89.0000 41 251 694 694.0 CC_Posterior 101.0552 12.4533 53.0000 129.0000 76.0000 42 252 314 314.0 CC_Mid_Posterior 100.2673 10.3702 63.0000 122.0000 59.0000 43 253 341 341.0 CC_Central 103.2910 10.9173 68.0000 125.0000 57.0000 44 254 354 354.0 CC_Mid_Anterior 105.7351 13.7075 66.0000 137.0000 71.0000 45 255 780 780.0 CC_Anterior 106.4097 12.6707 70.0000 132.0000 62.0000

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mask conversion from talairach
by Sam Cartmell 21 Jun '11

21 Jun '11

Hello Freesurfers, Using FS 4.5, I am attempting to do an ROI analysis based on activations seen in the group contrast. I'd like these ROI's to be a sphere around the peak voxel of each activation. Using a matlab program written by a colleague, I was able to generate spherical masks around the peak voxel in talairach functional space (i.e. no registration file is needed to view these masks overlayed on fsaverage and the masks have dimension 76 x 76 x 93 and voxel size 2 x 2 x 2 mm). I'd like to transfer these masks to native functional space (the same space as each subject's beta.nii file) so that I might extract the timecourse activity in matlab, and I was wondering 1) if what I list below is a valid way to do this transformation, and 2) if there is an alternative/superior way to accomplish this. After a lot of experimenting, the following series of commands appears to work: 1. mri_convert --input_volume group_sphere_mask.nii.gz --output_volume output1.nii.gz --ait Subject/mri/transforms/ talairach.xfm --this gives me an error message: ERROR MSGS -- INFO: Trying to get the source volume information from the transform name corRead(): can't open file Subject/mri/transforms/../orig/COR-.info INFO: Failed to find Subject/mri/transforms/../orig as a source volume. The inverse c_(ras) may not be valid. 2. mri_vol2vol --mov output1.nii.gz --targ Subject/bold/004/f.nii --regheader --o output2.nii.gz --interp nearest --this gives me a file with the right dimensions, but the values in the mask are no longer = 1, so then I use 3. mri_binarize -i output2.nii.gz -o output3.nii.gz --min .02 --where the min is a somewhat arbitrary threshold that seems to capture most of the voxels that were in the mask When I overlay this file on the subjects anatomical using: tkmedit Subject orig.mgz -overlay output3.nii.gz --reg Subject/bold/register.dat I get a mask which seems to be in the right place, but is no longer truly spherical and has the occasional voxel dropped from from the mask First and foremost, I would just like to know if this is valid, but I would also be eager to learn about any methods which might preserve the spherical shape and/or prevent any voxel dropout (and that don't give me error messages). Thanks, Sam Cartmell Research Assistant Visual Cognitive Neuroscience Laboratory, Dept Psychology Yale University

1 0

Re: [Freesurfer] error during mri_cvs_register
by Peter J. Molfese 21 Jun '11

21 Jun '11

Is there a reason that the Mac binaries are not available in 64-bit versions? On Jun 21, 2011, at 3:11 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Date: Tue, 21 Jun 2011 21:11:54 +0200 > From: Martin Kavec <martin.kavec(a)gmail.com> > Subject: Re: [Freesurfer] error during mri_cvs_register > To: David Brang <dbrang(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu, rspriti(a)nmr.mgh.harvard.edu > Message-ID: <BANLkTi=4zCQWpzUam0oLpmzGW6mO5fkb4A(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi David, > > FreeSurfer's binaries for MAC are still 32-bit and apparently cvs > tries to allocate more that is possible. The lines of the error code > below suggest that. I had the same problem and had to opt for x86_64 > linux binaries, where the cvs runs fine. It needs ~ 6 GB of memory and > takes ~ 2 days to finish. > > Regards, > > Martin > > 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 > > On Mon, Jun 20, 2011 at 11:34 PM, David Brang <dbrang(a)gmail.com> wrote: >> Thanks for the advice Priti, >> I deleted the old cvs files and re-ran but still no luck. I also tried a new >> subject on a different Mac (still 10.6.7) and received the same error. >> Thanks >> David >> >> On Mon, Jun 20, 2011 at 12:56 PM, <rspriti(a)nmr.mgh.harvard.edu> wrote: >>> >>> Hi David, >>> >>> I usually get PETSC errors when I have files from a previous unsuccessful >>> runs of cvs and mri_cvs_register is trying to overwrite the same set of >>> files. I've always found that deleting all the cvs related files before >>> starting mri_cvs_register from scratch usually solves the issue. You can >>> try doing that to see if it works for you. >>> >>> Thanks, >>> Priti >>> >>> >>>> 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 >>>> _______________________________________________ >>>> 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 >> >> >> 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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