Re: [Freesurfer] Re: problematic pial

sure, if you put it on the filedrop I'll try to take a look. Why did you smooth the volume? That might be the source of our trouble with it cheers, Bruce On Mon, 7 Apr 2008, Jamie Hanson wrote: Hi Jamie, it's impossible to judge surface accuracy from one slice. You need to move forwards an

Re: [Freesurfer] Re: problematic pial

Hi Jamie, it's impossible to judge surface accuracy from one slice. You need to move forwards and back a couple of slices to see if the surface is curving sharply out of plane. Can you explain a bit more about what is unique about this volume? I didn't really understand from your email. Is

Re: [Freesurfer] Data Discrepancies

Hi Jared, 10-30% is not that much if you are using different versions and looking at small structures (e.g. amygdala or entorhinal cortex). Why are you using different versions? That's definitely something to be avoided. cheers, Bruce On Mon, 7 Apr 2008, Jared Morton wrote: I am using Fre

Re: [Freesurfer] Estimating the difference in cortical thickness between two groups

Your interpretation of the beta.mgh file is correct. That contrast will compute the difference of the groups. Not sure what you mean by the "slope of the difference". doug jorge luis wrote: Hello all We are comparing the cortical thickness of two groups with the following fsgd file: GroupD

Re: [Freesurfer] Cortical parcellation

no, sorry, it's not that easy. We really expect the whole hemi to be there and there's no easy way to remove part of it Bruce On Mon, 7 Apr 2008 [EMAIL PROTECTED] wrote: Okey, thanks a lot! I have another question though: Will Freesurfer (in the automatic cortical parcellation) always try t

[Freesurfer] problematic pial

Hi Freesurfers- I was trying to run freesurfer on a study template and was having major problems with pial surface generation. Orig and Main surfaces seem to be ok, but there are major missing chinks in pial surface. Just to give some background, the template was being using for Diffeomorphic Imag

[Freesurfer] Data Discrepancies

I am using Freesurfer to analyze a set of brains of subjects with temporal lobe epilepsy. The brains are being run at two different locations. In addition, the brains at one location have been run on two different computers, with two different freesurfer builds. The problem that I am having is t

Re: [Freesurfer] Cortical parcellation

Okey, thanks a lot! I have another question though: Will Freesurfer (in the automatic cortical parcellation) always try to parcellate/label all of the cortex? I was wondering if a solution to the problem could be to either change and rename the ?h.curvature.buckner40.filled.deskian_killiany.2007-0

[Freesurfer] Estimating the difference in cortical thickness between two groups

Hello all We are comparing the cortical thickness of two groups with the following fsgd file: GroupDescriptorFile 1 Title Thickness-subj Class contr Class modif Input subj1 contr Input subj2 contr Input subj3 contr Input subj4 contr ... Input subj36 modif Input subj37 modif Input subj38