Freesurfer August 2006

freesurfer@nmr.mgh.harvard.edu

48 participants
74 discussions

TKMEdit error on Mac OS 10.4.7
by Kent Ogden 09 Aug '06

09 Aug '06

Hi, I have a brand new Macbook pro with the dual-core intel chip. I downloaded and installed the most recent verision of freesurfer. When I run the configuration script I get source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-tiger-stable-pub-v3.0.3 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast SUBJECTS_DIR /Applications/freesurfer/subjects FUNCTIONALS_DIR /Applications/freesurfer/sessions MINC_BIN_DIR /Applications/freesurfer/mni/bin MINC_LIB_DIR /Applications/freesurfer/mni/lib PERL5LIB /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 GSL_DIR /Applications/freesurfer/lib/gsl TCLLIBPATH /Applications/freesurfer/lib/tcltktixblt/lib MISC_LIB /Applications/freesurfer/lib/misc/lib tcsh: gcc: Command not found. tcsh: gcc: Command not found. FSL_DIR /Applications/freesurfer/fsl Which looks ok, except for not finding gcc. tksurfer seems to run fine, but tkmedit just gives an error: Kent% tkmedit bert orig.mgz X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 129 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 15 Current serial number in output stream: 15 Can anyone help me with this? Thanks . . . Kent Ogden PhD Associate Professor, Radiology SUNY Upstate Medical University 750 E. Adams Street Syracuse, NY 13210 email: ogdenk(a)upstate.edu voice: (315) 464-5083 fax: (315) 464-5095

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Bad File Descriptor?
by Jake Freimer 08 Aug '06

08 Aug '06

I am guessing that this is a general file error, not something specifically related to freesurfer, but was wondering if anyone had an idea on what might be wrong. 18 vertices at 20 distance writing curvature file /private/Network/Servers/dns2.bmap.ucla.edu/Volumes/BMC3/BMCUsers3/ascott/Documents/freesurfer/subjects/td21new/surf/lh.thickness tee: /private/Network/Servers/dns2.bmap.ucla.edu/Volumes/BMC3/BMCUsers3/ascott/Documents/freesurfer/subjects/td21new/scripts/recon-all.log: Bad file descriptor Darwin lion.bmap.ucla.edu 8.7.0 Darwin Kernel Version 8.7.0: Fri May 26 15:20:53 PDT 2006; root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Tue Aug 8 07:03:55 PDT 2006 Thanks -Jake

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Re: [Freesurfer] Feature request for tkmedit
by d.g.lawyer＠medisin.uio.no 08 Aug '06

08 Aug '06

As Jenni pointed out, tkmedit does ask you to save your edits when you exit using the file menu on the toolbar. I would like to see this feature extended so that it also asks when you close by clicking the x in the corner of the window. You only really need this kind of safety-check when you are tired, which is also the time when you are most likely to close a window by clicking the x in the big window you were just working in, instead of hunting for the file menu on the little tool window on your other monitor. Not that it has ever happened to me, by the way. I just read about it in a book, once.

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Feature request for tkmedit
by d.g.lawyer＠medisin.uio.no 08 Aug '06

08 Aug '06

Hi, It would be great if tkmedit would ask if you have saved your edits before closing. Any chance of getting this added? As it currently stands, it is easy to just press the little x in the corner of the tkmedit window and close it, without recording any of your work. Of course no-one does this when they are fresh, but after hours of editing one sometimes is in a state of rapturous bliss and forgets these little details.

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glutInit bug
by Don.Rojas＠UCHSC.edu 08 Aug '06

08 Aug '06

Dear List: I saw that there was a known issue with glutInit on Debian systems that caused problems with tksurfer. I just thought I'd report that although tksurfer (Freesurfer 3.0.3 stable) runs without error on my two Ubuntu systems (32 bit and 64 bit), I get the same sort of glutInit error message when I try to run scuba: scuba -s 0003 -v T1 Using /usr/local/freesurfer/lib/tcl/tkUtils.tcl Using /usr/local/freesurfer/lib/tcl/histolabel.tcl Using /usr/local/freesurfer/lib/tcl/scuba.tcl freeglut ERROR: Function <glutBitmapCharacter> called without first calling 'glutInit'. Will this issue also be addressed in 3.0.4.? Best, Don

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Freesurfer install error OS Tiger, GSL error
by Charles-Henri Malbert 07 Aug '06

07 Aug '06

Dear collegue, I was using Freesurfer 0.9 and I try to install freesurfer 3. The install went smoothly and I update the cshrc file. The launch of Xterm went fine and the postinstall generate no errors (i.e. the GSL lib was found at GSL_DIR). When trying to test the install using tkmedit bert orig.mgz an error was generated saying that the GSL lib was not found at pubsw (dyld: Library not loaded: /usr/pubsw/packages/ gsl/1.6/lib/libgsl.0.dylib). Indeed no pubsw folder was found at usr. I was using fink and gsl was already installed in sw folder as part of Amide installation (a gnu front end of Xmedcon). May be the problem was arround there? What's the problem Thanks in advance Charles-Henri Malbert DMV, Dr es Sci, HDR Directeur de Recherches UMR SENAH 35590 Saint-Gilles Tel: 02 23 48 50 71 Fax: 02 23 48 50 80

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Slackware 10.0.0
by Chacko Cherian 07 Aug '06

07 Aug '06

Hello all, I have a small query.Just wanted to know which stable Freesurfer version I should install for Linux Slackware 10.0.0 version. Has anybody experienced any issues usig this platform. Thanks in advance. Chacko Cherian. Arizona State University. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Recon all finished with errors, How do I see what errors?
by Jake Freimer 07 Aug '06

07 Aug '06

I was running autorecon2-cp and it said it finished with errors, below are the recon-all.log and recon-all-status.log, I couldn't figure out what the error is. Mon Aug 7 10:37:16 PDT 2006 #@# Intensity Normalization2 Mon Aug 7 10:37:16 PDT 2006 #@# Mask BFS Mon Aug 7 11:01:39 PDT 2006 #@# WM Segmentation Mon Aug 7 11:01:59 PDT 2006 Darwin lion.bmap.ucla.edu 8.7.0 Darwin Kernel Version 8.7.0: Fri May 26 15:20:53 PDT 2006; root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Mon Aug 7 11:12:31 PDT 2006 ...... #@# Mask BFS Mon Aug 7 11:01:39 PDT 2006 /private/Network/Servers/dns2.bmap.ucla.edu/Volumes/BMC3/BMCUsers3/ascott/Documents/freesurfer/subjects/td21new/mri \n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n threshold mask volume at 5 Talairach transform /usr/local/freesurfer/subjects/td21new/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /private/Network/Servers/dns2.bmap.ucla.edu/Volumes/BMC3/BMCUsers3/ascott/Documents/freesurfer/subjects/td21new/mri/transforms/talairach.xfm writing masked volume to brain.finalsurfs.mgz... #-------------------------------------------- #@# WM Segmentation Mon Aug 7 11:01:59 PDT 2006 \n cp wm.mgz wm.seg.mgz \n \n mri_segment -keep brain.mgz wm.seg.mgz \n preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM: 105.9 +- 5.5 [80.0 --> 125.0] GM: 70.1 +- 9.7 [30.0 --> 96.0] setting bottom of white matter range to 79.7 setting top of gray matter range to 89.4 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 4126 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2519 filled 2784 bright non-wm voxels segmented. 2121 diagonally connected voxels added... white matter segmentation took 10.4 minutes writing output to wm.seg.mgz... Darwin lion.bmap.ucla.edu 8.7.0 Darwin Kernel Version 8.7.0: Fri May 26 15:20:53 PDT 2006; root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Mon Aug 7 11:12:31 PDT 2006 Thanks -Jake

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Skull Stripping
by Derin Cobia 07 Aug '06

07 Aug '06

Hello, After having run -autorecon1 on all of my subjects I've noticed skullstripping has edited out the cerebellum/brainstem on some, but not on others. Because I'm not interested in these structures, can I just leave the files as is (i.e.-not bother adjusting the wsthreshold level, re-running, etc)? Or will I run into problems with the -autorecon2 & 3 processing streams down the line? Thanks again! -Derin

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surface format
by Anqi Qiu 07 Aug '06

07 Aug '06

Hi, Could you let me know the format of the surface generated by freesurfer? Is that easy to convert it to *.vtk? And also is the surface in the original subject space or in Talairach space? Thanks Anqi Qiu Center for Imaging Science The Johns Hopkins University

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Freesurfer August 2006