[Freesurfer] mri_surfcluster command syntax

Hi, An oddity re: command syntax for mri_surfcluster. The --ocp flag writes the file sig.cluster.mgh. However, when I also include the --cwsig flag the file sig.cluster.mgh is not generated. Currently I run the command twice, once to generate the sig.cluster.mgh, and once to generate the cluster

Re: [Freesurfer] cluster analysis with mri_glmfit

[EMAIL PROTECTED] wrote: Hi, I have a couple of specific questions regarding cluster analysis with mri_glmfit that weren't answered at the course the other week and on which the documentation is slightly vauge. My data includes continuous variables (age and IQ, matching the documentaion!) so

Re: [Freesurfer] mri_surfcluster command syntax

That's very wierd. Do you want to try the latest version and see if you get the same thing? I've copied it to: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfcluster doug [EMAIL PROTECTED] wrote: Hi, An oddity re: command syntax for mri_surfcluster. The --ocp flag wr

[Freesurfer] STG Volume

Hello all, My lab needs to obtain STG volumes for a bunch of minc files. I've been going through the wiki and found that recon-all has to be run to first convert the files into mgz after which it will automatically generate a file with the volumes. I ran it on one of our computers (P4 @ 3.8 Ghz

[Freesurfer] Autoseg and surface extraction

Dear Bruce, Does the autoseg information get used for surface extraction? For example, when autoseg classfies the ventricles and basalganglia, are the surface extraction routines supposed to treat these voxels as part of white matter and continue? Ideally at the end of the day any place where the

Re: [Freesurfer] STG Volume

sorry, you need to wait a bit longer. The time is variable depending on the brain, but 12-16 hours/hemisphere is pretty common. Bruce On Wed, 5 Jul 2006, Ajith Kumar U wrote: Hello all, My lab needs to obtain STG volumes for a bunch of minc files. I've been going through the wiki and found

Re: [Freesurfer] Autoseg and surface extraction

Hi Satra, yes, the aseg is used in the surface recon, but the thickness won't be identically zero there. We let the surface settle wherever it wants, but mask those regions out of group studies. I should probably write something one of these days to automatically generate a mask. It would be

Re: [Freesurfer] printing out from tksurfer and tkmedit

Thanks Don.That would be really useful. Chacko. --- Don Hagler <[EMAIL PROTECTED]> wrote: > If there is interest, I could post my shell script > for generating a tcl > script and running tksurfer (with an option to write > to rgb). I have > another one that will render all w files in a > part