[Freesurfer] about the label file

Hello: I select a region and save it to a label file named red.label. But I could't understand the data in this file. The follwing is part of this file. #!ascii label , from subject cengqinping vox2ras=TkReg coords=white 5690 31281 -51.356 -54.196 26.649 0.00 31282 -52.142 -54.229 2

[Freesurfer] error: mris compute white volume

Dear freesurfers, I get an error message while running recon-all on two on my subjects (on both version 4.02 and 4.05 on a CentOS linux station). It seems to be the same error that is described earlier this summer by Sky Raptentsetsang. The error message is: MrisComputeWhiteVolume: src (14, 721,

[Freesurfer] true-Talairach vs mni-Talairach?

Dear Freesurfers, I am a little bit confused about the talairach coordinates in Freesurfer. I have two diffrent versions of Freesurfer: 4.0.1 and 4.0.5. I opend brain.mgz in tkmedit and try to do the following things: when I type in Freesurfer 4.0.1 in the tkmedit-window some Talairach coordin

Re: [Freesurfer] about cortical thickness

Hi Tim, the thickness is stored in the ?h.thickness file for every vertex on each hemisphere (*not* for every voxel). YOu can convert it to an ascii format with mris_convert, or the aparc.stats file tabulates it by region. cheers, Bruce On Wed, 20 Aug 2008, [GB2312] ÀîÈÕ wrote: Hi: I hav

Re: [Freesurfer] true-Talairach vs mni-Talairach?

Hi Iris, this was a bug in 4.01. that we fixed in 4.0.5. cheers, Bruce On Wed, 20 Aug 2008, Steinmann, Iris wrote: Dear Freesurfers, I am a little bit confused about the talairach coordinates in Freesurfer. I have two diffrent versions of Freesurfer: 4.0.1 and 4.0.5. I opend brain.mgz in tk

Re: [Freesurfer] error: mris compute white volume

Christian, Updated mri_segstats and mris_wm_volume executables for centos 32/64bit can be downloaded from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable Nick On Wed, 2008-08-20 at 10:57 +0200, [EMAIL PROTECTED] wrote: > Dear freesurfers, > > I get an error message

[Freesurfer] Tksurfer rendering problem

Hello, I'm having an issue with tksurfer - whenever I try to load a surface, the display only shows scattered points (with the vaguely recognizable shape of the intended surface). I've noticed the following error that may be related to this: libGL error: open DRM failed (Operation not permitted)

Re: [Freesurfer] Tksurfer rendering problem

Hi Joao, is this true for any subject or only this one? cheers, Bruce On Wed, 20 Aug 2008, Joao Pereira wrote: Hello, I'm having an issue with tksurfer - whenever I try to load a surface, the display only shows scattered points (with the vaguely recognizable shape of the intended surface).

Re: [Freesurfer] Tksurfer rendering problem

Joao, Make sure your graphics driver is up to date. Also make sure that 'glxgears' runs properly on your system. That exercises the OpenGL X driver. Nick On Wed, 2008-08-20 at 16:37 +0100, Joao Pereira wrote: > Hello, > > I'm having an issue with tksurfer - whenever I try to load a surface, t

Re: [Freesurfer] brain orientation

Hi Margaret and Kathy, you *really* don't want to be trying to guess the orientation yourself as you are likely to get left/right wrong. Avi: have you moved data back and forth into freesurfer? cheers Bruce On Wed, 20 Aug 2008, Margaret Sheridan wrote: We are new users of freesurfer (linu

Re: [Freesurfer] brain orientation

Bruce, Yeah, I know about that danger. We are doing this on brains where we have a marker - a vitamin e capsule on the left side of the forehead. I'm most concerned about learning how to rotate the brains at all, right at the moment. Thanks (for the concern as well), Margaret On 8/20/08, Bruce

Re: [Freesurfer] brain orientation

Margaret, orient_mri is a gui tool which can be used to re-orient a volume, visually. for help, see: https://surfer.nmr.mgh.harvard.edu/fswiki/orient_mri Nick On Wed, 2008-08-20 at 16:33 -0400, Margaret Sheridan wrote: > Bruce, > > Yeah, I know about that danger. We are doing this on brains

Re: [Freesurfer] brain orientation

You can try using mri_convert with the -iid, -ijd, and -ikd options. I'll warn you now, this is not a fun thing to do, but once you figure it out for one, you can probably script it with the rest. The middle letter indicates the direction that is being manipulated. "i" is for left right, "j" is

[Freesurfer] Qdec Error

Hello, I am seeing the following error in the terminal window when I run an analysis in QDEC: INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous