On 6/20/06, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

I'll leave 2 for Doug. In 1. by segmentation do you mean the wm.mgz
volume? Or the cortical parcellation? If the latter, which one (as we
generate two by default).

cheers,
Bruce

On Tue, 20 Jun 2006, Jeffrey Spielberg
wrote:

> Hi, I had a couple of questions regarding cortical/subcortical segmentation-
>
> 1.  In our cortical segmentation we keep getting what look to be inaccurate
> segmentation of the rostral and caudal acc.  It looks some of what should be
> labeled as one of those two areas is getting labelled corpus callosum or
> "unlabelled subcortical" instead, sometimes fairly large chunks.  Does this
> indicate any problem earlier in the processing stream, and is there anything
> that can be done to prevent this?  If not I saw that both tksurfer and
> tkmedit can be used to edit the segmentation, what would be the easiest way
> to do this?
>
> 2.  When registering a freesurfer anatomical to Feat output (using
> reg-feat2anat) the registration seems to be somewhat inaccurate.
> Registering brainmask.mgz to our example_func using flirt has given us a
> better registration so far.  Since reg-feat2anat seems to use flirt in its
> registration I was wondering what the difference might be resulting from.
> Does reg-feat2anat use T1.mgz as it's reference scan, and if so is there any
> way to have it use brainmask instead, as that seems to give better results?
>
>
> Thanks,
> Jeff
>