Freesurfer April 2008

freesurfer@nmr.mgh.harvard.edu

67 participants
102 discussions

Centos 5 freesurfer GLX GLXBadLargeRequest - Install NVidia driver manually?
by Brian Hanna 24 Apr '08

24 Apr '08

Hi all, We are having a problem running tksurfer on several Centos 5 machines. We are getting the dreaded GLXBadLargeRequest and just the front sliver of the brain displayed. By installing the Nvidia driver manually, we made it work. We have one Centos 5 machine where it is working (machine01). That one machine has an Nvidia card and the Nvidia driver installed. We find that machine01 runs tksurfer correctly locally, and other machines can connect to machine01 with VNC and run tksurfer remotely on machine01. None of the other machines work correctly. Following up on the Nvidia driver difference, I notice that the Nvidia driver package includes a number of GL libraries. On the other machines, standard Centos 5 installs, I see: > $ ls -l /usr/lib*/libGL* > lrwxrwxrwx 1 root root 10 Jan 7 14:57 /usr/lib64/libGL.so -> > libGL.so.1 > lrwxrwxrwx 1 root root 12 Jan 7 14:57 /usr/lib64/libGL.so.1 -> > libGL.so.1.2 > -rwxr-xr-x 1 root root 492720 Nov 10 11:23 /usr/lib64/libGL.so.1.2 > lrwxrwxrwx 1 root root 11 Jan 7 14:57 /usr/lib64/libGLU.so -> > libGLU.so.1 > lrwxrwxrwx 1 root root 20 Jan 7 14:57 /usr/lib64/libGLU.so.1 -> > libGLU.so.1.3.060501 > -rwxr-xr-x 1 root root 526048 Nov 10 11:23 /usr/lib64/libGLU.so.1.3.060501 > lrwxrwxrwx 1 root root 12 Apr 23 14:49 /usr/lib/libGL.so.1 -> > libGL.so.1.2 > -rwxr-xr-x 1 root root 432016 Nov 10 11:24 /usr/lib/libGL.so.1.2 > lrwxrwxrwx 1 root root 20 Feb 3 16:07 /usr/lib/libGLU.so.1 -> > libGLU.so.1.3.060501 > -rwxr-xr-x 1 root root 524000 Nov 10 11:24 /usr/lib/libGLU.so.1.3.060501 I see (based on the modification time of the install) that there are several new libraries installed from Nvidia. That's a new libGL and 10mb libGLcore, and my standard libGL.so.1.2 has been zapped. > $ ls -l /usr/lib*/lib* | grep 09:21 > lrwxrwxrwx 1 root root 22 Apr 16 09:21 /usr/lib64/libGLcore.so.1 > -> libGLcore.so.100.14.11 > -rwxr-xr-x 1 root root 9777704 Apr 16 09:21 > /usr/lib64/libGLcore.so.100.14.11 > -rw-r--r-- 1 root root 661 Apr 16 09:21 /usr/lib64/libGL.la > lrwxrwxrwx 1 root root 10 Apr 16 09:21 /usr/lib64/libGL.so -> > libGL.so.1 > lrwxrwxrwx 1 root root 18 Apr 16 09:21 /usr/lib64/libGL.so.1 -> > libGL.so.100.14.11 > -rwxr-xr-x 1 root root 822960 Apr 16 09:21 /usr/lib64/libGL.so.100.14.11 > lrwxrwxrwx 1 root root 18 Apr 16 09:21 > /usr/lib64/libnvidia-cfg.so -> libnvidia-cfg.so.1 > lrwxrwxrwx 1 root root 26 Apr 16 09:21 > /usr/lib64/libnvidia-cfg.so.1 -> libnvidia-cfg.so.100.14.11 > -rwxr-xr-x 1 root root 127096 Apr 16 09:21 > /usr/lib64/libnvidia-cfg.so.100.14.11 > lrwxrwxrwx 1 root root 26 Apr 16 09:21 > /usr/lib64/libnvidia-tls.so.1 -> libnvidia-tls.so.100.14.11 > -rwxr-xr-x 1 root root 3016 Apr 16 09:21 > /usr/lib64/libnvidia-tls.so.100.14.11 > -r--r--r-- 1 root root 185148 Apr 16 09:21 /usr/lib64/libXvMCNVIDIA.a > lrwxrwxrwx 1 root root 26 Apr 16 09:21 > /usr/lib64/libXvMCNVIDIA_dynamic.so.1 -> libXvMCNVIDIA.so.100.14.11 > -rwxr-xr-x 1 root root 137944 Apr 16 09:21 > /usr/lib64/libXvMCNVIDIA.so.100.14.11 > lrwxrwxrwx 1 root root 22 Apr 16 09:21 /usr/lib/libGLcore.so.1 > -> libGLcore.so.100.14.11 > -rwxr-xr-x 1 root root 10080488 Apr 16 09:21 > /usr/lib/libGLcore.so.100.14.11 > -rw-r--r-- 1 root root 659 Apr 16 09:21 /usr/lib/libGL.la > lrwxrwxrwx 1 root root 10 Apr 16 09:21 /usr/lib/libGL.so -> > libGL.so.1 > lrwxrwxrwx 1 root root 18 Apr 16 09:21 /usr/lib/libGL.so.1 -> > libGL.so.100.14.11 > -rwxr-xr-x 1 root root 608400 Apr 16 09:21 /usr/lib/libGL.so.100.14.11 > lrwxrwxrwx 1 root root 26 Apr 16 09:21 > /usr/lib/libnvidia-tls.so.1 -> libnvidia-tls.so.100.14.11 > -rwxr-xr-x 1 root root 2352 Apr 16 09:21 > /usr/lib/libnvidia-tls.so.100.14.11 For a test, I temporarily copied the libraries and make the appropriate links on another machine - basically installing the driver manually. I find that now the entire brain displays and I don't get the GLXBadLargeRequest. I suppose I could have installed an Nvidia card and installed the driver to accomplish the same thing. You can use the -x option to the NVidia driver package to just extract it without running the installer. Be sure to check the LICENSE file, sections 2.1.2 and 2.1.3, before deciding how to proceed with this information. So the problem lies in functionality available in the Nvidia libGL (etc) libraries that is not available in the standard Centos 5 libGL. What GL/GLX libraries do I install on a non-Nvidia machine in order to run tksurfer? Does tksurfer depend specifically on having Nvidia cards or other proprietary drivers installed? The wiki states: > A 2GHz or faster processor, at least 2GB of RAM, and a 3D graphics > card (with a GPU and its own graphics memory) with accelerated OpenGL > drivers, is recommended. Freesurfer is highly CPU and memory intensive > (and moderately disk intensive), so concentrate on boosting those > performance aspects (more memory is better). Most modern video > graphics card will perform fine, but be aware that graphics cards that > use CPU memory as video memory will have a noticeably slow redraw rate. Thanks, Brian Hanna CMRR University of Minnesota

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Qdec display error
by Christine Ecker 24 Apr '08

24 Apr '08

Hi, I am using freesurfer v4.0.2 on Mac OS Tiger and am getting a qdec error message: WARNING: Marker for class Main was invalid And ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWW....., line 1182 VtkKWQdecApp : TclTkerror: Invalid command ... "vtkTemp249" .... I have substituted to old version of the script fsgdfPlot.tcl by a newer version that was posted online : ## fsgdfPlot.tcl ## ## CVS Revision Info: ## $Author: nicks $ ## $Date: 2008/01/03 13:45:36 $ ## $Revision: 1.24.2.2 $ ,but the problem still occurs. I would be very grateful for any ideas what the problem could be. Thanks very much, Christine

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SurfaceRAS space
by Michael Harms 24 Apr '08

24 Apr '08

Hello, I need to determine the transform between the surface coordinates between FS and the surface generated using some of the tools from JHU. I think that I have a handle on this, but just wanted to confirm a couple things. 1) First, the "voxel to ras transform" returned by 'mri_info' is the transform between a 0-based volume index DEFINED IN THE AXES OF THAT VOLUME'S ORIENTATION (as also returned by mri_info) to a "ras" space with origin at the center of the physical space spanned by that volume, correct (provided that you have not specified an alternative "ras" center as part of an 'mri_convert' command)? That is, say you have a rawavg.mgz volume created with a plain vanilla 'mri_convert' command on an Analyze volume (.img, .hdr) having the default Analyze orientation (hist.orient = 0, axial slice direction). This rawavg.mgz volume will have an 'mri_info' orientation of "LAS". And you have the corresponding orig.mgz volume with a (conformed) orientation of "LIA". THEN, the "voxel to ras transform" indicated for these volumes is NOT to an identical "ras" space, correct? (Namely, there will be a translation between the two "ras" spaces, due to the different orientations of the rawavg.mgz and orig.mgz, correct?) 2) The "SurfaceRAS" space of the vertices of the actual FS surfaces is always defined relative to the "conformed" volume with "LIA" orientation, correct? 3) Given (1) and (2), it is necessary to account for axes orientation of any non-conformed (i.e., non-LIA) volumes as part of the transformation between that volume representation and "SurfaceRAS" of the actual surfaces, since the "ras" center of the volume will shift by 1 voxel in physical space when you reverse the orientation of a given axis (given the use of a 0-based volume indexing scheme). Correct? Hope my questions are clear. I know that these various transformations can be tricky to get just right. 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: mharms(a)wustl.edu --------------------------------------------------------------------

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mri_ca_register
by Damian Jenkins 24 Apr '08

24 Apr '08

In addition to this we have several datasets here that have a couple of subjects failing with: Killed ERROR: mri_ca_register with non-zero status Linux jalapeno14 2.6.20-1.2320.fc5 #1 SMP Tue Jun 12 18:50:49 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux I see from the new 4.0.3 release notes that there is a fix for mri_ca_register for Darwin but all our errors have been on Linux. Could this be the same problem? D Dr Damian Jenkins Department of Clinical Neurology Oxford University

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Talairach QA check
by Damian Jenkins 24 Apr '08

24 Apr '08

You'll see we have a few Qs! We have been having problems with a couple datasets with patients who have severe atrophy (MS and Alzheimer's) where they fail in autorecon1 with the Talairach QA check. The registrations look fine so I was wondering what other problems might cause this check to fail. Is there a simple way to bypass the Talairach QA step in recon-all -autorecon1 if we are satisfied with the registration? Damian Dr Damian Jenkins Department of Clinical Neurology Oxford University

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FA registration problems
by Damian Jenkins 24 Apr '08

24 Apr '08

We are currently attempting to check the FA registration of each subject within an MS study group using the following command: tkregister2 --s fsaverage --surf white --reg /Volumes/Data/magnims/group_study/P??-??/dti_analysis/fa-tal.nii.reg --mov /Volumes/Data/magnims/group_study/P??-??/dti_analysis/fa-tal.nii However, this generates the following error message despite there being an orig.mgz in the fsaverage directory: ERROR: could not find orig as either mgz or COR Any ideas on what the problem might be? Thanks Damian Dr Damian Jenkins Department of Clinical Neurology Oxford University

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Freesurfer source code
by Petros Petrosyan 22 Apr '08

22 Apr '08

Hi I found via google that the freesurfer is open source and wanted to download the sources. I found one following URL http://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide. The sources are available at CVS repository which requires USERname and MACHINEname to access them. I am wondering if I can download the sources ? If yes please send me the instructions how to download them. If your project is not open source, please let me know. Thanks Best regards Petros Petrosyan LONI UCLA

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grad_unwarp error
by Bill Monaco 22 Apr '08

22 Apr '08

Hi, I'm in the stable 4 environment of FreeSurfer and am getting an error when I try to grad_unwarp a volume that comes out of unpacksdcmdir. The rror I get is: gradfilename is /autofs/space/windu_006/users/grad_unwarp_bash_MartinosCenter/grad_unwarp_tables/avanto.gwv. Loading... Unwarp data loaded. slice 1/128 9.1e-05 ??? Error using ==> interp3 V must be a 3-D array. Error in ==> unwarp_resample at 206 im1vec = interp3(imvol,C1,R1,S1,interp_method); Error in ==> convert_unwarp_resample at 211 [volout, Mout] = unwarp_resample(vol,M,size_out,Mout,Mdc,unwarpflag,jacflag,0,interp_method,inflag,thruflag,gradwarpfile); >> >> ERROR: output file not created I think the problem is the dimensions of the volume I'm trying to unwarp are off. When I type: mri_info flash30.mgz I see: type: MGH dimensions: 256 x 256 x 128 x 8 voxel sizes: 1.0000, 1.0000, 1.3300 type: SHORT (4) fov: 256.000 dof: 0 Any suggestions as to the best way to get around this problem? Thanks, Bill -- Bill Monaco Research Assistant MGH East - CNY 149 149 13th Street - 2271 Charlestown, MA 02129 617-726-9128

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Re: [Freesurfer] Autoredraw
by Julien Dubois 20 Apr '08

20 Apr '08

so, what I'd like to be able to do when I'm working remotely and each redraw takes ~10-15s, is: load everything I need (curvature, labels, change label colors, overlays, ...) and only redraw once when everything I want is on the picture. some superfluous redraws in any case: - when I click right to get rid of clicked vertices, it would be nice to do without that too. - when I click outside a selected label Double redraws: - when I load a label - when I define a label - when I load a patch - after I make a plane cut The list isn't exhaustive but I think these are the ones that have bothered me most. Maybe there should just be an option whereby it never redraws unless you ask for it manually. In any case, no need to apologize, this is a really useful and well implemented piece of software, so thank you! - Julien

1 0

Autoredraw
by Julien Dubois 20 Apr '08

20 Apr '08

Hi I'm working on tksurfer installed on a server and therefore it takes time to display the whole volume each time I draw a label, change its color, ... is there a way to prevent tksurfer from redrawing at each change, and redraw manually when needed? I tried the autoredraw button in the view menu but that doesn't do much. Thank you. - Julien Dubois

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Freesurfer April 2008