Re: [Freesurfer] QDEC and Slicer3

2008-05-27 Thread Nick Schmansky
Pedro, As yet, there is no documentation for it. It is just a small subset of the functionality found in the Qdec application distributed with Freesurfer, so using freesurfer's qdec is the preferred route at this point in time. Nick On Mon, 2008-05-26 at 18:16 -0300, Pedro Paulo de Magalhães O

Re: [Freesurfer] tksurfer display broken

2008-05-27 Thread Paul Raines
This maybe the composite issue if the NVIDIA driver is in use. Edit your /etc/X11/xorg.conf file and put in it: Section "Extensions" Option "Composite" "Disable" EndSection and restart On Tue, 27 May 2008, Krish Subramaniam wrote: Others ( Paul, Nick) might chip in with a much better

Re: [Freesurfer] freesurfer version 3.0 ?

2008-05-27 Thread Nick Schmansky
Lars, It is v3.0.0. The date should be March 2006. You can find out release dates to tie to version numbers here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Nick On Tue, 2008-05-27 at 16:27 +0200, Lars M. Rimol wrote: > Hi, > We have a dataset that was processed (by somebody else)

Re: [Freesurfer] White Matter Regional Volumes

2008-05-27 Thread Doug Greve
Try it on the wmparc.stats file, not the wmparc.mgz file. doug [EMAIL PROTECTED] wrote: My name is Jennifer as well, and I work in the same lab as Jennifer Bramen, who originally wrote to you, below. I am writing while she's out of town to follow up on your reply below. Mainly, I am a litt

[Freesurfer] White Matter Regional Volumes

2008-05-27 Thread hranilovich
My name is Jennifer as well, and I work in the same lab as Jennifer Bramen, who originally wrote to you, below. I am writing while she's out of town to follow up on your reply below. Mainly, I am a little confused by your suggestion to use asegstats2table command, because the resultant text fi

Re: [Freesurfer] tksurfer display broken

2008-05-27 Thread Krish Subramaniam
Others ( Paul, Nick) might chip in with a much better answer but my guess is your problem might be related to this thread earlier on the list.. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07324.html --Krish On May 27, 2008, at 11:30 AM, Juranek, Jenifer wrote: Hi, I recen

[Freesurfer] tksurfer display broken

2008-05-27 Thread Juranek, Jenifer
Hi, I recently encountered a problem with tksurfer display (worked perfectly fine a couple of weeks ago). The only change I've made to my linux (centOs 5) system is the recent installation of MATLAB r2008a. Just a note: This was *not* a fun process since the MATLAB 2008a install required depreca

[Freesurfer] freesurfer version 3.0 ?

2008-05-27 Thread Lars M. Rimol
Hi, We have a dataset that was processed (by somebody else) with an old freesurfer version and we need to find out exactly which version was used. We have a freesurfer_3.0 directory (and a freesurfer-Linux-centos4-stable-v3.0-full.tar.gz download) with a build-stamp.txt that says: freesurfer-Linux-

Re: [Freesurfer] cortical thickness

2008-05-27 Thread Bruce Fischl
no, we do it on a vertex basis. It's detailed on the wiki cheers, Bruce On Tue, 27 May 2008, Feng-Xian Yan wrote: Hi, I have some questions about cortical thickness. What method does freesurfer calculate the cortical thickness? Can freesurfer provide the cortical thickness value at each vox

Re: [Freesurfer] Color scheme settings frustratration

2008-05-27 Thread Marie Schaer
Martin, I made that specific figure with scuba, where you can overlay with a multicolor scale. Howevere, when you load the pial surface and overlay in tksurfer (set the minimum at 1, the mean around 3 and the maximum between 5 and 6), you can get a pretty nice red-orange-yellow color. M