Re: [Freesurfer] Analysis question

2008-01-09 Thread Bruce Fischl
Hi Corey, you can try smoothing the individual data, but of course you won't have the power that you have in a group study (which is why you do the group study in the first place). cheers, Bruce On Wed, 9 Jan 2008, Corey Keller wrote: Hi, I have a quick and hopefully simple question.

[Freesurfer] Gray Matter Mask - twist on previous post

2008-01-09 Thread Emily Trittschuh
Dear Group, Back in April, Anil Roy posted a question about methods to generate a gray matter mask that can be fed into AFNI . . . I'm wondering if the opposite can be done? Can a functional mask made in AFNI be fed easily into Freesurfer? Currently this mask is saved as a NIFTI dataset.

Re: [Freesurfer] Gray Matter Mask - twist on previous post

2008-01-09 Thread Bruce Fischl
Hi Emily, is it a volume or surface functional map? If volume, I think it should be pretty straightforward to sample it onto the surface with mri_vol2surf then go from there. There is probably a way to do this in SUMA also. cheers, Bruce On Wed, 9 Jan 2008, Emily Trittschuh wrote: Dear

[Freesurfer] segmentation of brain of age 8-13

2008-01-09 Thread BumSeok Jeong
Dear freesurfer experts, I got uncorrected segmentation results, especially occipital cortex, from brain of age 8-13. I found similar problem in adult brain in freesurfer mailing list and the resolving answer like below. use the control points with the mri_ca_normalize flag as part of the aseg.

Re: [Freesurfer] segmentation of brain of age 8-13

2008-01-09 Thread Bruce Fischl
Hi, we don't in general use the aseg.mgz for cortical stuff, so if it look inaccurate, but the ?h.white and ?h.pial surfaces look accurate then I wouldn't worry about it. It's hard to diagnoe without any images though. cheers, Bruce On Thu, 10 Jan 2008, BumSeok Jeong wrote: Dear