Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

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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having problem in running recon-all...
by Shahabuddin Ansari 07 Aug '06

07 Aug '06

Hello, I am having problem in running the following command: recon-all -i 2996926_02.img -s 2996926_02 I used to run the command before without any problem. Recently my linux has been updated to suse version, would that be a source of problem. The console display the following error: INFO: SUBJECTS_DIR is /ensc/IMAGE/opt/FREESURFER/subjects Actual FREESURFER_HOME /ensc/IMAGE/opt/FREESURFER Linux ilpc5 2.6.13-15.10-bigsmp #1 SMP Fri May 12 16:36:41 UTC 2006 i686 i686 i386 GNU/Linux mri_convert: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_convert: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_normalize: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_watershed: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_segment: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_fill: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_tessellate: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_smooth: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_inflate: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_sphere: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_fix_topology: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_euler_number: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_make_surfaces: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mris_register: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mrisp_paint: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_label2label: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_em_register: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_ca_normalize: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_ca_register: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory mri_ca_label: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory /ensc/IMAGE/opt/FREESURFER/subjects/2996926_02 mri_convert /ensc/IMAGE4/PROJECTS/HD_AYLWARD/DATA/PATIENTDATA/SHAHAB/2996926_02/2996926_02.img /ensc/IMAGE/opt/FREESURFER/subjects/2996926_02/mri/orig/001.mgz mri_convert: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory Linux ilpc5 2.6.13-15.10-bigsmp #1 SMP Fri May 12 16:36:41 UTC 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Sun Aug 6 19:08:34 PDT 2006 Shahab --------------------------------- Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail Beta.

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Problem copying subject directories
by Henry Lütcke 05 Aug '06

05 Aug '06

Hi, I ran autorecon-all on a Suse10.0 computer and it finished fine. when I copy the respective subject directory to another computer (Suse10.1) I can no longer view the surfaces with tksurfer (only a very tiny part is displayed; see attachment). I can view the volume in tkmedit fine and the surface is displayed on the computer where the analysis has been run. any ideas what might be causing this problem? thanks a lot, Henry

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Freesurfer