[Freesurfer] cortical parcellation in anterior cingulate region

Hello everybody, Regarding the troubles raised in the mailing list and on the release notes about the anterior cingulate being misclassified with curvature.buckner40.filled.desikan_killiany, I would like to know if you have any updated version of the atlas available? In my subjects, most

[Freesurfer] (no subject)

phi, when I run the qdec amp; command, the error show as below:/pp[EMAIL PROTECTED]:~gt; qdec amp;br /[1] 10941br /[EMAIL PROTECTED]:~gt; qdec.bin: error while loading shared libraries: libexpat.so.0: br /cannot open shared object file: No such file or directorybr //ppnbsp;I do't knownbsp; how

Re: [Freesurfer] cortical parcellation in anterior cingulate region

wow, that's awful. I don't think we usually see it be this bad. If you post this subject on our website we'll take a look On Mon, 25 Jun 2007, Marie Schaer wrote: Hello Bruce Rahul, Indeed in my sample of subjects it's more the corpus callosum directly with the frontal superior, and the

[Freesurfer] long delay before tksurfer launches

Hello, Apologies for cross-posting (this list and martinos-tech), but I think that by posting here I might be able to reach a few more people who may have had the problem before and solved it. I have been experiencing very long load-up times, when running tksurfer. It can take up to 6 or 7

Re: [Freesurfer] long delay before tksurfer launches

strace shows you the system calls being made by the program. When it's hanging for a long time, note the last few lines of output from strace and let us know what those are. The last one will be the call that is taking so long to finish. On Mon, Jun 25, 2007 at 11:56:00AM -0400, Robert Levy

Re: [Freesurfer] (no subject)

QDEC has not been officially released yet -- soon! [EMAIL PROTECTED] wrote: hi, when I run the qdec command, the error show as below: [EMAIL PROTECTED]:~ qdec [1] 10941 [EMAIL PROTECTED]:~ qdec.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No

RE: [Freesurfer] Segmentation

Hi Bruce, Thank you for your quick response. Our problem, actually, is that when we visualize the aseg.mgz volume (with color-coded subcortical structures) we see that WM is classified as GM (left circle around insula in the figure) and GM is classified as WM (right lower circle in the figure).

RE: [Freesurfer] Segmentation

Hi Antonio, that's why we we use the surfaces for white matter and cortical gray matter volume. cheers, Bruce On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote: Hi Bruce, Thank you for your quick response. Our problem, actually, is that when we visualize the aseg.mgz volume (with

[Freesurfer] Cortical surface tessellation and smoothing

Dear list, Is there a paper or any documentation describing how freesurfer tessellate and smooth cortical surfaces? In particular, does freesurfer use any specific variety of marching cube isosurface algorithm? Regular surface smoothing (like the Laplacian smoothing) may cause undesired

Re: [Freesurfer] Cortical surface tessellation and smoothing

Hi Kai, it was described in the Dale, et al. 1999 paper in NeuroImage, or maybe part in that and part in the 2nd part of it (Fischl et al., 1999 also NeuroImage). They are both on our wiki (surfer.nmr.mgh.harvard.edu/fswiki). We don't use marching cubes, but a custom tesselation algorithm.

RE: [Freesurfer] problems with -clean-bm flag

Hi Antonio, What is the complete command you are using the -clean-bm flag with? Jenni _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gallo, Antonio (NIH/NINDS) [F] Sent: Monday, June 25, 2007 7:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer]