yes, pick control points in freesurfer and run autorecon2-cp On Tue, 13 Mar 2007, Anil Roy wrote:
The brain ran fine and the segmentation looks good for most parts. However, for some regions of the temporal lobe the white matter segmentation is not very good. I think this has more to do with the intensity correction than the skull strip.
Is there any way to improve the intensity correction when feeding the brain from AFNI. Right now, I use 3duniformize in AFNI and again use nu in Freesurfer. Any specific flags in Freesurfer that may help?
Thanks,
Anil.
On 3/7/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
it should be okay, although any TIV estimates from the talairach won't be accurate.
On Wed, 7 Mar 2007, Anil Roy wrote:
Hi all,
Is Freesurfer going to generate all surfaces properly if I feed in a
skull
stripped brain to begin with starting from stage 1. In other words, is
there
going to be a problem if the orig.mgz is skull stripped. I checked the results after autorecon1 and the brainmask.mgz had a decent contrast.
The
xfm was also accurate.
The brain had poor contrast(and a format that Freesurfer wouldn't
recognize)
so I had AFNI do the skull strip and intensity correction and then fed
in
that brain to recon-all.
Thanks,
Anil.