[Freesurfer] Doubt about GM and thickness

2010-05-26 Thread Kelly Silva
Hello, I'm doing regression analyses with cortical thickness at the level of voxel. Should I correct the total GM volume by introducing this parameter as a confounding variable? Shoud I include the intracranial volume as an additional nuisance variable? If positive, I assume that these variabl

[Freesurfer] missing gaussian curvature file

2010-05-26 Thread Ana Catarino
Hello, I was trying to run a qdec analysis on Gaussian curvature and got the following error message: Error in Analyze: Couldn't open file $SUBJECTS_DIR/AS1/surf/lh.white.K.fwhm10.avgsubject.mgh I get the same error message on mean curvature analysis. Any ideas? Thanks, Ana Catarino __

Re: [Freesurfer] Recon failing during topology correction

2010-05-26 Thread Bruce Fischl
Hi Michael, looks like this defect has about 60K vertices in it, which is almost have a typical surface. Something is dramatically wrong. Look at the ?h.orig and see if it includes skull or cerebellum, or if there is some huge hole/handle in the ?h.orig.nofix. cheers Bruce On Wed, 26 May 2010

[Freesurfer] Gyral region centroids?

2010-05-26 Thread Dankner, Nathan (NIH/NIMH) [F]
Hi all, I am looking to get the centroids of the Desikan parcellation gyral regions to calculate distance. Any ideas on how to go about doing this? Thanks, Nathan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvar

Re: [Freesurfer] Gyral region centroids?

2010-05-26 Thread Bruce Fischl
distance between what and what? You could certainly load them into matlab and do it that way. Bruce On Wed, 26 May 2010, Dankner, Nathan (NIH/NIMH) [F] wrote: > Hi all, > > I am looking to get the centroids of the Desikan parcellation gyral regions > to calculate distance. Any ideas on how to

[Freesurfer] mac installation problems

2010-05-26 Thread Ed Vessel
Hi folks - I just installed Freesurfer on my Mac (OSX 10.5.8, quad-core intel xeon). The environment variables appear to be set up properly. >source ~/.tcshrc freesurfer-Darwin-leopard-ppc-stable-pub-v4.5.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_H

Re: [Freesurfer] mac installation problems

2010-05-26 Thread Nick Schmansky
use the mac leopard intel freesurfer distribution (it appears you are using the PowerPC distribution). n. On Wed, 2010-05-26 at 18:41 -0400, Ed Vessel wrote: > Hi folks - > > I just installed Freesurfer on my Mac (OSX 10.5.8, quad-core intel > xeon). The environment variables appear to be set

[Freesurfer] color wheel woes

2010-05-26 Thread Chris Said
Hi, I know that there have been questions about the color wheel in the past, and that future versions of tksurfer will resolve some of the issues. But in the meantime, I was wondering if I could get some help with the existing version: (1) Does anybody have access to good images of the color