Re: [Freesurfer] PETSC ERROR
Hi David, Have you downloaded the updates of mri_cvs_register from http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes ? We found some bugs in the orginial 5.1 release and put the fixed versions at the above. Let me know if that still does not solve the problem. --Lilla On Tue, 21 Jun 2011, David Brang wrote: 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 = 10 elapsed = 0.307 seconds element count = 1457735 count inserted = 20 elapsed = 0.44 seconds element count = 3996981 count inserted = 30 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
[Freesurfer] mri_convert PD
Hello all,
I'm attempting to use mri_convert in order to match the slice size and
thickness of T2 and PD images to the Freesurfer T1 images, after converting
the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like
${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/T2/T2_like_norm.nii.gz
And having no problems. However, using the same code for the PD images I'm
arriving at a bus error each time (output below). Is there any possible work
around for this?
(freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0)
---
bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz
--like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.nii.gz
mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl 003_S_0907_M00/mri/norm.nii.gz
--like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_norm.nii.gz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 003_S_0907_M00/PD/PD.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 2.05103e-10, 0)
j_ras = (-2.05103e-10, -1, 0)
k_ras = (-0, -0, 1)
reading template info from volume 003_S_0907_M00/mri/norm.nii.gz...
INFO: transform src into the like-volume: 003_S_0907_M00/mri/norm.nii.gz
Bus error
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Re: [Freesurfer] launchpad help
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-35006-20110508-105030-353000/353000-04-01.dcm -mail chin...@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-35006-20110508-105030-353000/353000-04-01.dcm -mail chin...@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Paul Rainesemail: 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 ___ Freesurfer mailing list Freesurfer@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] transforms/talairach_with_skull.lta during autorecon1 and autorecon2 - is it a bug or a feature
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 ___ Freesurfer mailing list Freesurfer@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] Volume-based stream: SupraTentorial Volume and Lesion-Mask
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.righ...@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, 215645.00, 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 4416544165.0 Left-Lateral-Ventricle19.7155 16.3746 0.89.89. 2 5 2806 2806.0 Left-Inf-Lat-Vent 38.3263 15.7951 0.83.83. 3 7 1365713657.0 Left-Cerebellum-White-Matter 81.6728 7.880419. 104.85. 4 8 5824758247.0 Left-Cerebellum-Cortex66.2938 9.300914. 102.88. 5 10 7895 7895.0
Re: [Freesurfer] mri_convert PD
if you file drop these volumes we'll take a look
Bruce
On Wed, 22 Jun 2011, G.
William Chapman IV wrote:
Hello all,
I'm attempting to use mri_convert in order to match the slice size and
thickness of T2 and PD images to the Freesurfer T1 images, after converting
the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like
${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/T2/T2_like_norm.nii.gz
And having no problems. However, using the same code for the PD images I'm
arriving at a bus error each time (output below). Is there any possible work
around for this?
(freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0)
---
bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz
--like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.nii.gz
mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl 003_S_0907_M00/mri/norm.nii.gz
--like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_norm.nii.gz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 003_S_0907_M00/PD/PD.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 2.05103e-10, 0)
j_ras = (-2.05103e-10, -1, 0)
k_ras = (-0, -0, 1)
reading template info from volume 003_S_0907_M00/mri/norm.nii.gz...
INFO: transform src into the like-volume: 003_S_0907_M00/mri/norm.nii.gz
Bus error
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: [Freesurfer] Two timepoints - same subject, correlation matrix
Hi, So I think I found the solution - (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical) reg-feat2anat aseg2feat or aparc2feat New question: Is there anyway to combine aseg2feat and aparc2feat? i.e. get all subcortical and cortical segmentations registered to functional space? Thanks, S On 06/21/11, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Sudhin, this looks like an AFNI question. Have you tried posting to the AFNI list? doug Sudhin A. Shah wrote: On Jun 17, 2011, at 6:25 PM, Sudhin A. Shah sut2...@med.cornell.edu mailto:sut2...@med.cornell.edu sut2...@med.cornell.edu wrote: 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) (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html%29) @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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (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 (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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) -- Sudhin A. Shah Postdoctoral Fellow Laboratory of Cognitive Neuromodulation Weill Cornell Medical College, NY,NY (212) 746-4514 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Two timepoints - same subject, correlation matrix
Got it : aseg2feat --feat featdir --seg aparc+aseg On 06/22/11, Sudhin A. Shah sut2...@med.cornell.edu wrote: Hi, So I think I found the solution - (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical) reg-feat2anat aseg2feat or aparc2feat New question: Is there anyway to combine aseg2feat and aparc2feat? i.e. get all subcortical and cortical segmentations registered to functional space? Thanks, S On 06/21/11, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Sudhin, this looks like an AFNI question. Have you tried posting to the AFNI list? doug Sudhin A. Shah wrote: On Jun 17, 2011, at 6:25 PM, Sudhin A. Shah sut2...@med.cornell.edu mailto:sut2...@med.cornell.edu sut2...@med.cornell.edu wrote: 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) (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html%29) @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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (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 (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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) -- Sudhin A. Shah Postdoctoral Fellow Laboratory of Cognitive Neuromodulation Weill Cornell Medical College, NY,NY (212) 746-4514 -- Sudhin A. Shah Postdoctoral Fellow Laboratory of Cognitive Neuromodulation Weill Cornell Medical College, NY,NY (212) 746-4514 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] transforms/talairach_with_skull.lta during autorecon1 and autorecon2 - is it a bug or a feature
Hi Michael thanks for the info, we'll look into this. We are aware of some of the issues with running multiple times, but need to look into it further when we find the time Bruce On Wed, 22 Jun 2011, Michael Scheel wrote: 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 ___ Freesurfer mailing list Freesurfer@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] Error running recon-all
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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] launchpad help
Hi Chindhuri remove the -l nodes=1:opteron from your command line. Also, you probably want to send emails like this to h...@nmr.mgh.harvard.edu in the future, as they are Martinos-specific. cheers Bruce On Wed, 22 Jun 2011, Chindhuri Selvadurai wrote: 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-35006-20110508-105030-353000/353000-04-01.dcm -mail chin...@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-35006-20110508-105030-353000/353000-04-01.dcm -mail chin...@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Paul Rainesemail: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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] Questions about the Freesurfer course
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 fslcou...@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 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Questions about the Freesurfer course
do you mean the FreeSurfer course? Or the FSL/FreeSurfer course? In either case you get hands-on experience and personal help in going through data. cheers Bruce On Wed, 22 Jun 2011, Mu Xue wrote: 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 fslcou...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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] find corresponding coordinates of verteces
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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Error running recon-all
Hi Antonella we usually view the ?h.white and ?h.pial surfaces over the norm.mgz and the aseg.mgz and check them all for accuracy. If things are not where you think they should be, then you need to take one of the interventions documented on the wiki. cheers Bruce On Wed, 22 Jun 2011, Antonella Kis wrote: 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] PETSC ERROR
Hi Lilla, Yes, sadly the problem still persists. The strangest part is that the same error occurred when I tried to process bert (mri_cvs_register --mov bert) using the VirtualBox Ubuntu package for FS on Windows. My only guess (as suggested by one of the other users) is that it's a problem with 32-bit binaries not having access to 4gigs of RAM, as both FS for the Virtual Box and for Mac are 32 bit. I've installed 64-bit Linux versions into virtual boxes on both my Windows and Mac computers and haven't received any errors yet (~24 hours of processing) so this will hopefully get around the problem. Has there been any movement compiling FS with 64-bit binaries for Mac? Thanks for the help David On , Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi David, Have you downloaded the updates of mri_cvs_register from http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes ? We found some bugs in the orginial 5.1 release and put the fixed versions at the above. Let me know if that still does not solve the problem. --Lilla On Tue, 21 Jun 2011, David Brang wrote: 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 = 10 elapsed = 0.307 seconds element count = 1457735 count inserted = 20 elapsed = 0.44 seconds element count = 3996981 count inserted = 30 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
[Freesurfer] How to obtain volume of specific structure
Hi all: After all recon-all -all processing has been completed for all subjects ,I want to obtain volume of specific structure of each subject(e.g., the volume of Caudate Nucleus). But i have no idea about it,Are there some tools or commands that can help? I hope you can give me some suggestions . Thanks! ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] How to obtain volume of specific structure
Take a look in aseg.stats file -- iOS 4.3 Em 22/06/2011, às 23:09, ZhiLiangLong lagosslong1...@163.com escreveu: Hi all: After all recon-all -all processing has been completed for all subjects ,I want to obtain volume of specific structure of each subject(e.g., the volume of Caudate Nucleus). But i have no idea about it,Are there some tools or commands that can help? I hope you can give me some suggestions . Thanks! ___ Freesurfer mailing list Freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
