Freesurfer

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30078 discussions

Odd tkmedit behavior
by Dan Dillon 04 Mar '08

04 Mar '08

Dear FreeSurfers, I have overlaid group data on the fsaverage brain, and find that when I type Talairach coordinates into tkmedit (e.g., 9.90 -36.64 -14.15), the cursor jumps to a nearby but different location (e.g., 9.8 -36.1 -10.1). Any ideas what could be causing this trouble? Thanks! Dan Dillon

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question about generating wmparc.stats
by Teddy Youn 04 Mar '08

04 Mar '08

Hi again, I had a quick question about generating wmparc.stats. I have tried to run recon3 with the -wmparc flag and have encountered an error where ?h.smoothwm is not being read even though my /surf folder has the files. Below is the output of what occurs in my xterm. We have v4.0.2 of FS on Leopard 10.5.2. Thanks in advance, -t ============================================================================== recon-all -autorecon -wmparc -no-isrunning -subjid St14-Initial INFO: SUBJECTS_DIR is /Volumes/ZetaData/Teddysfolder/CorrectedBrainsSiemens/TBISt14 Actual FREESURFER_HOME /Applications/freesurfer -rwxrwxrwx 1 teresa teresa 2712975 Mar 3 17:41 /Volumes/ZetaData/Teddysfolder/CorrectedBrainsSiemens/TBI/St14/St14-Initial/scripts/recon-all.log Darwin 0-1d-4f-48-96-f4.dyn.utdallas.edu 9.2.0 Darwin Kernel Version 9.2.0: Tue Feb 5 16:13:22 PST 2008; root:xnu-1228.3.13~1/RELEASE_I386 i386 #-------------------------------------------- #@# Sphere lh Mon Mar 3 17:43:27 CST 2008 /Volumes/ZetaData/Teddysfolder/CorrectedBrainsSiemens/TBI/St14/St14-Initial/scripts \n mris_sphere ../surf/lh.inflated ../surf/lh.sphere \n $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ $Id: mrisurf.c,v 1.557.2.5 2007/12/10 20:20:29 nicks Exp $ reading original vertex positions... MRISreadVertexPositions(../surf/lh.smoothwm): surfaces differ. Main: 194252 ver s 390408 faces, smoothwm: 188404 verts 378044 faces No such file or directory MRISreadOriginalProperties: could not read surface file smoothwm No such file or directory Darwin 0-1d-4f-48-96-f4.dyn.utdallas.edu 9.2.0 Darwin Kernel Version 9.2.0: Tue Feb 5 16:13:22 PST 2008; root:xnu-1228.3.13~1/RELEASE_I386 i386 recon-all exited with ERRORS at Mon Mar 3 17:43:30 CST 2008 Doris Duke Clinical Research Fellow '07-'08 North Texas TBI Research Center UT Southwestern Medical Center at Dallas Warren Alpert School of Medicine at Brown University, MD '09 Teddy.Youn(a)utsouthwestern.edu (401)-714-2847

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Re: [Freesurfer] tksurfer tcl
by Graham Wideman 04 Mar '08

04 Mar '08

What caption are you refering to? Graham At 3/4/2008 07:44 AM, you wrote: >Hello, > >Is there a way to adjust the caption (at least turn it on and off) in a >tcl script. I couldn't find any information on the wiki. > >Cheers, >Dan > > >-- > > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] tksurfer tcl
by Graham Wideman 04 Mar '08

04 Mar '08

Hmmm, well since the menus are implemented in tksurfer.tcl, it might be possible to add some tcl to that file (actually it already has code to daisy-chain to user-provided extra code on startup), to implement some means to control caption on/off by a later script. Not known by me: how the normal tksurfer mechanism to run a user script interacts with tksurfer.tcl. But it should be easy to discover. Graham At 3/4/2008 02:44 PM, Daniel Wakeman wrote: >Hi, > >Sorry, As in View>>Caption. In the menu bar. > >Thanks >Dan >> What caption are you refering to? >> >> Graham >> >> At 3/4/2008 07:44 AM, you wrote: >>>Hello, >>> >>>Is there a way to adjust the caption (at least turn it on and off) in a >>>tcl script. I couldn't find any information on the wiki. >>> >>>Cheers, >>>Dan >>> >>> >>>-- >>> >>> >>>_______________________________________________ >>>Freesurfer mailing list >>>Freesurfer(a)nmr.mgh.harvard.edu >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > >-- >

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Desikan atlas brains
by joel bruss 04 Mar '08

04 Mar '08

Hello- Is there anywhere to download the 40 subjects used to create the Desikan atlas? If so, do these datasets contain all the transform/FreeSurfer files from start to finish? Thanks, Joel

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mri_watershed Error: GLOBAL region of the brain empty
by özlem özmen okur 04 Mar '08

04 Mar '08

Hello, I have the same error (mri_watershed Error: GLOBAL region of the brain empty !) as described Micheal Harms' mail (below) which left I guessed as unanswered. Any help would be appreciated. Thanks, Ozlem OZMEN-OKUR Bogazici Univ. Biomedical Engineering Istanbul-TURKEY [Freesurfer] autorecon1 errors Michael Harms Tue, 26 Feb 2008 13:31:48 -0800 Hello, We recently just ran 80 elderly brains through -autorecon1 using FS v4.0.2, and encountered 3 different types of errors that we are not entirely sure how to handle: (1) During mri_normalize of 1 subject we encountered: SPLINE_CUBIC_SET - Fatal error! The number of data points N must be at least 2. The input value is 1. The FS archive indicates to check the talairach transform given this error, but the talairach.xfm appears fine for this subject (as assessed using tkregister2). (2) During mri_watershed of 1 subject: Sorting... mri_watershed Error: Problem in the COG calculation This subject had a slightly warped talaraich.xfm, but I think more relevantly, its talairach_with_skull.lta was way off. (3) During mri_watershed of 5 subjects: mri_watershed Error: GLOBAL region of the brain empty ! For all 5 of these subjects, the talairch_with_skull.lta also had obvious problems. RE (1): Any insight would be appreciated. RE (2) and (3): I suspect that we should try running with the -no- wsgcaatlas flag, so that talairach_with_skull.lta is longer used by mri_watershed. Should we then substitute the -wsatlas flag instead? (Its not clear to me which atlas is used when that particular flag is included). Last, I thought you might be interested in these errors, because they directly relate to my recent question regarding the robustness of talairach_with_skull.lta. At least during the -autorecon1 (i.e., initial) creation of this lta file, it appears that there is some possibility of a bad talairach_with_skull registration (6 of 80 in this particular subject set). thanks, 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: [EMAIL PROTECTED] --------------------------------------------------------------------

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tksurfer tcl
by Daniel Wakeman 04 Mar '08

04 Mar '08

Hello, Is there a way to adjust the caption (at least turn it on and off) in a tcl script. I couldn't find any information on the wiki. Cheers, Dan --

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finding WM hypointensities
by Thomas Doering 04 Mar '08

04 Mar '08

Hello, i wonder if there is a possibility to identify the recognized WM hypointensities with tkmedit - something like labeling the WM hypointensities. Thanks for help, Thomas

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tksurfer overlay scale bar label colors
by Scott Gorlin 03 Mar '08

03 Mar '08

Hi, When I display an overlay scale bar in tksurfer, the labels for the scale bar are displayed in black on a black background. Obviously, this is completely unusable since I cannot read them! They are there, however, because if I move the surface over so that it underlies the scale bar, the text shows up (in black) just fine. Some time ago the text was rendering in blue, which I thought was an odd choice but gave no further thought to it until I noticed the text disappear completely. Now, it seems like a bug to me, but unfortunately I did not notice exactly when the switched occurred. Unless there is some setting buried somewhere to control the text color? I'd love to just set it to white and not deal with this again... I have upgraded both my os and my graphics drivers recently so I wonder if that broke something. The only clue I have is that I know the newest ATI drivers run on AIGLX instead of XGL, could that cause any errors? I'm seeing this in both FS 3 and 4: tksurfer --all-info on my v.4 returns: ProgramName: tksurfer.bin ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2008/03/03-22:12:05-GMT BuildTimeStamp: Sep 17 2007 17:25:01 CVS: $Id: tksurfer.c,v 1.276.2.5 2007/09/16 23:37:27 greve Exp $ User: scott Machine: Renoir Platform: Linux PlatformVersion: 2.6.22-14-generic CompilerName: GCC CompilerVersion: 30200 tksurfer --all-info on my v.3 returns: ProgramName: tksurfer.bin ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 08/03/03-22:14:40-GMT CVS: $Id: tksurfer.c,v 1.183.2.11 2007/01/04 22:30:38 nicks Exp $ User: scott Machine: Renoir Platform: Linux PlatformVersion: 2.6.22-14-generic CompilerName: GCC CompilerVersion: 30200 My system: Ubuntu 7.10 (recently upgraded from 7.04) pentium 4 fglrxinfo returns: display: :0.0 screen: 0 OpenGL vendor string: ATI Technologies Inc. OpenGL renderer string: RADEON X600 Series OpenGL version string: 2.1.7281 Release glxinfo | grep direct returns: direct rendering: Yes xdpyinfo | grep GL returns: ATIFGLEXTENSION ATIFGLRXDRI GLX SGI-GLX Thanks a lot, Scott

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Desikan training sets
by joel bruss 03 Mar '08

03 Mar '08

Is there a place to download the 40 brains used in the creation of the Desikan atlas? If so, would the training data have all of the FreeSurfer data (directories and transform files) so that one could easily create ones own parcellation scheme and create a new brain?

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