[Freesurfer] surface format
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] having problem in running recon-all...
Shahab, libgsl is included with the freesurfer distribution, and a path is setup to point to it when the freesurfer setup script is 'sourced'. What is displayed when you type: source $FREESURFER_HOME/SetUpFreeSurfer.csh GSL_DIR should be one of the lines. Switching to suse should not be a problem. Nick On Sun, 2006-08-06 at 19:16 -0700, Shahabuddin Ansari wrote: > 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. > ___ > 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
Re: [Freesurfer] surface format
Anqi, The default surface file generated by freesurfer is a proprietary format, but the freesurfer utility 'mris_convert' will convert to ascii and vtk formats (among others). Two examples: mris_convert rh.pial rh.pial.asc creates an ascii file of triangle vertices and faces, and: mris_convert rh.pial rh.pial.vtk creates a vtk formated file. See: mris_convert --help and also: http://www.grahamwideman.com/gw/brain/fs/surfacefileformats.htm Coords are in subject space (not talairach space, but a mris_convert allows specify a transform file). Nick On Mon, 2006-08-07 at 10:13 -0400, Anqi Qiu wrote: > 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 > > > > ___ > 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
Re: [Freesurfer] surface format
Hi Anqi, the surface is a binary format. You can convert it to ascii using mris_convert (the ascii format is defined on our wiki). They are in native space, not talairach. cheers, Bruce On Mon, 7 Aug 2006, Anqi Qiu wrote: 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 ___ 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
[Freesurfer] Slackware 10.0.0
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Skull Stripping
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Skull Stripping
Hi Derin, the subcortical segmentation will fail unless you correct it, as the registration will try and align a model with a cerebellum to a brain without one. sorry. Bruce On Mon, 7 Aug 2006, Derin Cobia wrote: 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 ___ 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
[Freesurfer] Recon all finished with errors, How do I see what errors?
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 [EMAIL PROTECTED] Intensity Normalization2 Mon Aug 7 10:37:16 PDT 2006 [EMAIL PROTECTED] Mask BFS Mon Aug 7 11:01:39 PDT 2006 [EMAIL PROTECTED] 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 .. [EMAIL PROTECTED] 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... # [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Recon all finished with errors, How do I see what errors?
Hi Jake, Did it write out the wm.seg.mgz file (would be in the subjects mri directory)? Is it possible that you either don't have write permissions in that directory or that you are out of disk space? Jenni On Mon, 7 Aug 2006, Jake Freimer wrote: 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 [EMAIL PROTECTED] Intensity Normalization2 Mon Aug 7 10:37:16 PDT 2006 [EMAIL PROTECTED] Mask BFS Mon Aug 7 11:01:39 PDT 2006 [EMAIL PROTECTED] 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 .. [EMAIL PROTECTED] 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... # [EMAIL PROTECTED] 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 ___ 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
Re: [Freesurfer] Slackware 10.0.0
Chacko, For Slackware 10, you should probably use the rh9 build of freesurfer, as rh9 uses the v2.4 kernel, as does Slackware 10. Nick On Mon, 2006-08-07 at 11:10 -0700, Chacko Cherian wrote: > 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 > ___ > 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
Re: [Freesurfer] Freesurfer install error OS Tiger, GSL error
On the Mac, libgsl is included with Freesurfer in the directory /Applications/freesurfer/lib/gsl. Can you confirm that your LD_LIBRARY_PATH and DYLD_LIBRARY_PATH environment variables contain those paths? That is, examine the output of: env | grep LD_LIBRARY Also, make sure that these vars do not contain paths to the other versions of GSL. You can make sure of this by typing: unsetenv LD_LIBRARY_PATH unsetenv DYLD_LIBRARY_PATH before 'sourcing' the Freesurfer setup script. On Sat, 2006-07-29 at 23:36 +0200, Charles-Henri Malbert wrote: > 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 > > > ___ > 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
[Freesurfer] TKMEdit error on Mac OS 10.4.7
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: [EMAIL PROTECTED] voice: (315) 464-5083 fax: (315) 464-5095 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
