Re: [Freesurfer] help with mris_ca_label

is that *_trans_toSulc.gcs or *.atlas2002_simple.gcs? Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] >>> "Brian T. Quinn" <[EMAIL PROTECTED]> 11/01/05 7:38 PM >>> canonical surfac

Re: [Freesurfer] help with mris_ca_label

*.atlas2002_simple.gcs is Christophe's atlas that we used before the current dev version. On Wed, 2 Nov 2005, Sasha Wolosin wrote: is that *_trans_toSulc.gcs or *.atlas2002_simple.gcs? Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway

[Freesurfer] subcortical segmentation

Hi, As mentioned in a previous message, running the subcortical segmentation takes 10-15 hours, primarily because of the Cannonical Registration (mri_ca_register) step. However, one the freesurfer papers (Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Br

Re: [Freesurfer] subcortical segmentation

Hi Eli, no, I wouldn't. After that paper we developed a nonlinear registration procedure, which is the long one, that helps things considerably. cheers, Bruce On Wed, 2 Nov 2005, Eliezer Kahn wrote: Hi, As mentioned in a previous message, running the subcortical segmentation takes 10-15 ho

[Freesurfer] area file

Hello everybody! I have one question about how surface areas are calculated by mris_anatomical stats (release2004). I noticed that the ?h.area file may contain the portion of area corresponding to each different vertex. Actually, the sum of all these areas is around 7'500mm^2 for one hemisphere

Re: [Freesurfer] area file

We found a problem with this computation about a year ago (11/12/2004 to be specific). I think I sent an email about it to the list. Any releases prior to that date will have this error in the area computations. Can you try it with a more recent release? Marie Schaer wrote: Hello everybo

Re: [Freesurfer] area file

I tried with mris_anatomical_stats from freesurfer-Linux-rh9-v2.1 and I obtained exactly the same result for total surface area as in matlab with the sum of all the triangles, thanks for the advice! In the mean time I was just wondering how folding index returned by mris_anatomical_stats is calc

Re: [Freesurfer] help with mris_ca_label

I'm having trouble specifying the output file when running mris_ca_label- should it be in the surf folder or somewhere else? (output below) Thanks, Sasha [EMAIL PROTECTED] surf]$ pwd /home/wolosin/subjects/dec1877J_prac/surf [EMAIL PROTECTED] surf]$ mris_ca_label dec1877J_prac rh rh.sphere.reg /fr

Re: [Freesurfer] help with mris_ca_label

Hi Sasha, it gets written into the label dir by default. Are you sure that directory exists (should be at the same level as surf) Bruce On Wed, 2 Nov 2005, Sasha Wolosin wrote: I'm having trouble specifying the output file when running mris_ca_label- should it be in the surf folder or some

Re: [Freesurfer] area file

Hi Marie, the folding indices are taken from one of the original Van Essen and Drury papers. Sorry I don't have the ref handy. Bruce On Wed, 2 Nov 2005, Marie Schaer wrote: I tried with mris_anatomical_stats from freesurfer-Linux-rh9-v2.1 and I obtained exactly the same result for total s

Re: [Freesurfer] area file

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9278543&query_hl=1 I got it, thank you very much! Marie Quoting Bruce Fischl <[EMAIL PROTECTED]>: > Hi Marie, > > the folding indices are taken from one of the original Van Essen and Drury > papers.

Re: [Freesurfer] help with mris_ca_label

thanks, I created a label directory and that solved the problem. It looks like all our subjects are missing a label directory. Do you know why that might happen? Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (

Re: [Freesurfer] help with mris_ca_label

no. The mksubjdirs script should create a label dir. On Wed, 2 Nov 2005, Sasha Wolosin wrote: thanks, I created a label directory and that solved the problem. It looks like all our subjects are missing a label directory. Do you know why that might happen? Sasha Wolosin Research Assistant D

[Freesurfer] (no subject)

Hi, I have a script that basically opens up tksurfer and tkmedit for manual editing, and then runs recon-all stage2 once you’re done editing. We recently tried to run the script on a different computer with the same freesurfer distribution, and got an error I’m not used to seeing.   It sa

[Freesurfer] Re: Freesurfer Digest, Vol 21, Issue 3

Regarding this issue with the old version of mris_anatomical_stats, will problems with rh.area effect any of the other results? Or are there any bugs effecting other anatomical stats besides rh.area? Message: 2 Date: Wed, 02 Nov 2005 12:58:06 -0500 From: Doug Greve <[EMAIL PROTECTED]> Subject: Re

Re: [Freesurfer] (no subject)

Hi Aaron, First, is it something simple and annoying like that your script doesn't look for an orig.mgz volume (vs. the 'orig' which was standard until fairly recently)? I have needed to edit my scripts to accommodate for this. okay! On Wed, 2 Nov 2005, Goldman, Aaron (NIH/NIMH) wrote:

[Freesurfer] freesurfer + fsl

Hi All, I have installed Freesurfer for Mac OS X (2 Oct 2005) on my system (running 10.4.2) - thanks for the OS X release! Unfortunately, fsl doesn't work after the installation of Freesurfer. This is the error message I get when I try to open the fsl GUI: Error in startup script: no suita

[Freesurfer] automated parcellation

Dear Freesurfers, We have used the automated parcellation (Fischl et al, 2004) in several subjects and noticed in some cases labeling of the lateral part of a gyrus (i mean the part that's visible on the folded surface), as belonging to a sulcus. The example I have in mind is the labeling of a