Freesurfer November 2007

freesurfer@nmr.mgh.harvard.edu

54 participants
74 discussions

OT - animating ?h.pial or aparc+aseg
by Martin Kavec 07 Nov '07

07 Nov '07

Hi, sorry to bring an off topic, but I could not find a solution myself. I was asked to prepare a short fly-by animation of a ?h.pial for a TV who interviewed my boss last week. Would you have any recommendation on how to do that? The ?h.pial is a mesh, which is ideal, because the surface of the pial would be nice and smooth. I tried to export aparc+aseg to Analyze and read it into OsiriX, where I can easily produce the animation, but the surface was not smooth, as one would expect. So that is not the solution. Has anyone experience with this kind of task? Thanks, Martin

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OpenGL
by Daniel Wakeman 06 Nov '07

06 Nov '07

Hello, I am configuring a Freesurfer installation for two different types of computers (headless servers and workstations). For both sets of computers we want any non-OpenGL commands that are run to first go through python scripts which load balance (these are working fine); however we have directly included the standard tkmedit* tksurfer* tkregister2* scuba* scuba2* and qdec* in the bin directory of freesurfer for the workstations. We still do not seem able to get these applications to work. Are there some dependencies, which I am missing for each of these besides tkmedit.bin etc.? Thank You, Dan

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spmregister on 64 bit
by Doug Greve 06 Nov '07

06 Nov '07

I have spmregister (and spmregister-sess) working on 64 bit machines. The fix is to set the FS_SPMREG_MATLAB to point to the 7.0.1 version of matlab. In the NMR Center, you can just: setenv FS_SPMREG_MATLAB /usr/pubsw/common/matlab/7.0.1/bin/matlab You can do this without affecting the version of matlab that you normally use. This will also work on 32 bit machines. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Matrix ill-conditioned and "yellow brain"
by Juergen Haenggi 06 Nov '07

06 Nov '07

Dear Freesurfer experts We have two problems with FS statistics. One problem occurred when using mri_glmfit: Matrix condition is 11198.7 ERROR: matrix is ill-conditioned or badly scaled, condno = 11198.7 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. I inspected the FSGD file but did not find any error! There was a suggestion in the FS archives to look at the design matrix for significant off-diagonal values but the design matrix (X.mat) was not produced Any idea where the problem is? In another contrast the sig.mgh file produced huge values and the whole brain is colored yellow (see attachment). What happens here? Thanks a lot in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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error during watershed
by Matt Colvin 05 Nov '07

05 Nov '07

Hello freesurfer gurus. Recently I was trying to do a fix on a brain that appeared to have a bad skull strip. The T1 was fine but the brainmask volume came out almost totally black, with the surfaces confined to some fuzziness in the corner (appearing very strange in tkmedit). I attempted to fix the skullstrip by adjusting the watershed, using version 4 to remain consistent with our other subjects for whom we did recon1 with version 4 to get better talairachs. Below is the last part of the log. Any ideas? ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=196 y=119 z=233 r=13 first estimation of the main basin volume: 10195 voxels mean intensity too low ! Modification of the image: intensity*10.67 first estimation of the COG coord: x=196 y=119 z=233 r=13 first estimation of the main basin volume: 10195 voxels mri_watershed Error: Interpolation problem in the white matter curve analysis Linux rainmaker 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Thu Nov 1 16:25:31 CDT 2007

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Qdec question
by Xiangchuan Chen 05 Nov '07

05 Nov '07

Hi all, I am using Qdec to examine the anatomical differences between two groups of subjects. The surface-based measures I can select are thickness, area, area.pial, sulc, curv, and jacobian_white. Could anybody tell me what anatomical features the later three (sulc, curv, and jacobian_white) actually measure? Thanks in advance, Xiangchuan Chen

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Re: [Freesurfer] COR-files
by Xiangchuan Chen 05 Nov '07

05 Nov '07

Hi Chris, I guess you might click on "Save Main Volume As...", and then "OK". In this case, 257 COR- files would be created in the /mri folder. I happened to do it once, and redid the whole edit work. Xiangchuan ======== Start Of Original Message ======== Date: 2007-11-05 Time: 10:05:47 From: Chris Watson (Christopher.Watson(a)childrens.harvard.edu) To: freesurfer(a)nmr.mgh.harvard.edu (freesurfer(a)nmr.mgh.harvard.edu) Subject: [Freesurfer] COR-files >Hello, this is my first time using Freesurfer. > >I was making some edits to the brainmask.mgz and T1.mgz volumes, and >saved them and left Friday evening. I would like to continue making >edits today. How do I open these volumes so that they include the edits >I made? When I saved, 256 COR-files were created in the >SUBJECTS_DIR/<subject>/mri directory. Do I use mri_convert? If so, what >is the syntax? > >mri_convert --in_type cor COR-001 --out_type spm ??? > >Thanks, >Chris >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ========= End Of Original Message =========

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COR-files
by Chris Watson 05 Nov '07

05 Nov '07

Hello, this is my first time using Freesurfer. I was making some edits to the brainmask.mgz and T1.mgz volumes, and saved them and left Friday evening. I would like to continue making edits today. How do I open these volumes so that they include the edits I made? When I saved, 256 COR-files were created in the SUBJECTS_DIR/<subject>/mri directory. Do I use mri_convert? If so, what is the syntax? mri_convert --in_type cor COR-001 --out_type spm ??? Thanks, Chris

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recon-all error
by Anil Roy 04 Nov '07

04 Nov '07

Hi All, I got the following error while running recon-all on a set of dicoms. It seems to be a problem with the intensity correction stage but I can't get it to work. Any help is appreciated. Thanks, Anil. [root@wonglinux1 freesurfer]# recon-all -i /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702-0002-0001-0001.dcm -s O-07-002 -autorecon-all INFO: SUBJECTS_DIR is /mnt/win/MRI_data/MWIN4/Freesurfer Actual FREESURFER_HOME /usr/local/freesurfer Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386 GNU/Linux WM removal version /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002 mri_convert /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702- 0002-0001-0001.dcm/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz mri_convert /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702- 0002-0001-0001.dcm/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz reading from /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702- 0002-0001-0001.dcm... Getting Series No INFO: Found 162 files in /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom INFO: Scanning for Series Number 2 Scanning Directory INFO: found 160 files in series INFO: loading series header info. RunNo = 1 INFO: sorting. INFO: (192 256 160), nframes = 1, ismosaic=0 FileName /mnt/win/MRI_data/MWIN4/O-07-002/anatomical_dicom/9702-0002-0001-0001.dcm Identification NumarisVer syngo MR 2006T 4VB12T ScannerModel TrioTim PatientName 9702 Date and time StudyDate 20070328 StudyTime 113239.765000 SeriesTime 114403.109000 AcqTime 113640.352512 Acquisition parameters PulseSeq tfl3d1 Protocol MPRAGE AXIAL PhEncDir ROW EchoNo 0 FlipAngle 9 EchoTime 3.36 InversionTime 900 RepetitionTime 2300 PhEncFOV 192 ReadoutFOV 256 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 256 NImageCols 192 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 101.4164 183.6733 -63.6460 VolRes 1.0000 1.0000 1.0000 VolDim 192 256 160 Vc -0.9991 0.0030 -0.0434 Vr -0.0000 -0.9977 -0.0681 Vs -0.0435 -0.0680 0.9967 VolCenter 2.0258 50.8135 3.2105 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2300.00, TE=3.36, TI=900.00, flip angle=9.00 i_ras = (-0.999053, 0.00296272, -0.0434174) j_ras = (-2.12178e-10, -0.99768, -0.0680798) k_ras = (-0.0435184, -0.0680153, 0.996735) writing to /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Nov 4 16:38:15 CST 2007 Found 1 runs /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig/001.mgz /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/rawavg.mgz /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002 mri_convert /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/rawavg.mgz /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz --conform mri_convert /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/rawavg.mgz /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz --conform reading from /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/rawavg.mgz... TR=2300.00, TE=3.36, TI=900.00, flip angle=9.00 i_ras = (-0.999053, 0.00296272, -0.0434174) j_ras = (-2.12178e-10, -0.99768, -0.0680798) k_ras = (-0.0435184, -0.0680153, 0.996735) Original Data has (1, 1, 1) mm size and (192, 256, 160) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 4 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz... mri_add_xform_to_header -c /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Sun Nov 4 16:38:45 CST 2007 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri /usr/local/freesurfer/bin//mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $ Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386 GNU/Linux Sun Nov 4 16:38:45 CST 2007 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 tmpdir is ./tmp.mri_nu_correct.mni.7437 /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7437/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7437/nu0.mnc Can't find the talairach xform '/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/transforms/talairach.xfm TR=2300.00, TE=3.36, TI=900.00, flip angle=9.00 i_ras = (-1, -1.52311e-10, -6.04436e-10) j_ras = (5.26148e-10, 2.33896e-09, -1) k_ras = (1.65039e-10, 1, 5.09647e-09) writing to ./tmp.mri_nu_correct.mni.7437/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Sun Nov 4 16:39:03 CST 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.7437/nu0.mnc ./tmp.mri_nu_correct.mni.7437/nu1.mnc [root@wonglinux1:/mnt/win/MRI_data/MWIN4/Freesurfer/O-07-002/mri/] [2007-11-04 16:39:03] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_7482/ ./tmp.mri_nu_correct.mni.7437/nu0.mnc ./tmp.mri_nu_correct.mni.7437/nu1.imp Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Sun Nov 4 16:39:07 CST 2007

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ReconAllDevTable
by Michael Harms 02 Nov '07

02 Nov '07

Hello, Just a couple miscellaneous items/suggestions regarding the very helpful ReconAllDevTable: 1) The entry for -inflate2 currently indicates that ?h.white is the input file. This should be ?h.smoothwm instead. 2) It might be helpful to add a line to the -skullstrip stage indicating the 'mri_em_register' command that preceeds 'mri_watershed' so as to indicate where the "talairach_with_skull.lta" file comes from that is used as part of 'mri_watershed' in v4.0.1 3) Do you have "archived" versions of the ReconAll table that are appropriate for previous stable releases? If so, it would be great if the wiki contained links to those. If not, it might be helpful to create such "snapshots" of the ReconAll flow table so that there is a convenient place to access the process flow that is most accurate for previous (non-developmental) releases. cheers, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Freesurfer November 2007