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Some questions related to f mri_surfcluster.
by Zhen Zonglei 05 Mar '08

05 Mar '08

Hi，all: I have some questions related to the command of mri_surfcluster (and mri_volcluster). The help of this command says cwsig option can give the cluster-wise sig-map, but vwsig option will give vertex-wise sig-map. What is the exact meaning of these options? Does every voxel in one specific cluster have a common p value in cwsig-map (refer to significance of the cluster)? Does every voxel in one specific cluster have different p values in vwsig-map (refer to significance of the voxel)? Should the p value of one specific voxel in vwsig-map equal to its p value in the original sig-map (non-corrected)? I want to display the corrected cluster map, but hope every voxel in a cluster have a p value of itself. how to implement this function? Thanks in advance. Zonglei Zhen

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Cortical thickness map
by Juergen Haenggi 05 Mar '08

05 Mar '08

Dear FS experts I overlaid the thickness file of a single subject (see attachment). When I showed the colour bar there are no values presented and the colour bar appears in blue and red (as in F- or t-contrast) with grey in between. Why there are grey islands and how to present the thickness values in mm that corresponds to the colour of colour bar? Thanks 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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mris_thickness_diff ERROR
by Scott Beeman 04 Mar '08

04 Mar '08

Hello, I am trying to use Xiao Han's ThicknessRepeatability methods for a longitudinal study. I have successfully completed step one, which is rigid registration of the pre and post scans, but I am having problems with step 2. This step uses the mris_thickness_diff function to compute the thickness difference map. I use the following command, as suggested by Xiao Han: mris_thickness_diff -xform $SUBJECTS_DIR/1001/mri/transforms/1001_to_1001a.lta \ -src_type curv \ -out $SUBJECTS_DIR/1001/surf/lh.thickness_diff.mgh \ -nsmooth 0 \ -abs -S 1001 \ -L $SUBJECTS_DIR/1001/surf/lh_thickness_diff.log \ $SUBJECTS_DIR/1001/surf/lh.white \ $SUBJECTS_DIR/1001/surf/lh.thickness \ $SUBJECTS_DIR/1001a/surf/lh.white \ $SUBJECTS_DIR/1001a/surf/lh.thickness The function successfully reads the surfaces, but if fails when trying to apply the LTA xform to align surface 1 to surface 2. The terminal states: INFO:try to get src info from transform. ERROR: ComputeDifferenceNew: MHTfindClosestVewrtexNo returned nnindex=-1, which is invalid I have experienced this error for multiple subjects and have been unable to get past it. I am unsure of what the nnindex is and why it is -1. Any help on this issue would be greatly appreciated. Thanks. -Scott Beeman

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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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