Re: [Freesurfer] Interpretation of cortical thickness result

2007-10-16 Thread Bruce Fischl
so you see huge loss of gm volume, but not of thickness? What happens to the surface area? And what does "huge" mean in this context? What kind of #s are you seeing, and what kind of means and stds to you see in your controls? On Tue, 16 Oct 2007, Martin Kavec wrote: Thanks for the answer,

Re: [Freesurfer] Interpretation of cortical thickness result

2007-10-16 Thread Martin Kavec
Thanks for the answer, Bruce. My aim is to assess severity of cortical atrophy and I am trying to find optimal SINGLE parameter for that, i.e. GM thickness, GM volume, or something else. What I do is, I take mean thickness of a parcel A of a GM from ?h.aparc.stats for the my patient and compar

Re: [Freesurfer] Interpretation of cortical thickness result

2007-10-16 Thread Bruce Fischl
Hi Martin, when you look at the mean difference between this subject and controls you mean it's within a std of the controls? That's not terribly surprising, as there is a lot of normal neuroanatomical variability. Is it below the mean over much of the cortex? Is the overall mean thickness re

[Freesurfer] Talairach transformations in tkmedit and tkregister2

2007-10-16 Thread Dr. Claudia Wheeler-Kingshott
Hi, We have a problem with the Talairach transformations. When we load the talairach.mgz file using tkmedit the axial and coronal orientations are swapped and displaced in the window. The puzzling thing is that if we use tkregister2, the registration is very good. Any idea of why? I found a

RE: [Freesurfer] Problems with make_average_subject

2007-10-16 Thread jorge luis
I have solved the problem by comments in the make_average_subject, make_average_volume and make_average_surface scripts the line: limit descriptors unlimited This line of code was not present in the FS v.3.0.5 --- jorge luis <[EMAIL PROTECTED]> escribió: > Hello all > > I am trying to bu

[Freesurfer] Interpretation of cortical thickness result

2007-10-16 Thread Martin Kavec
Hi folks, I have been puzzled for a while with the results from couple of my subjects. They all have clearly visible cerebral atrophy (says neuroradiologist). I ran them through FS-4.0.1 and aseg.stat gives me, as expected, severe loss of gray matter (and others as well) as follows: GM ICV nor