Hi Judit,
there is a white matter parcellation that is run by default called
wmparc.mgz. Anything else is future work. The pial surface misplacement
is usually a result of the white matter being wrong, but the intervention
depends on the problem, so we'd need to see the example. As for the
edit
Bruce Fischl wrote:
> Hi Judit,
>
> all the edits will be kept, so that shouldn't be a problem. It's hard
> to diagnose the wm segmentation without looking at a volume, but if
> they are really hyperintense you may need to manually fill them in in
> the wm.mgz. As for mri_cc, you should use aseg
Hi Judit,
all the edits will be kept, so that shouldn't be a problem. It's hard to
diagnose the wm segmentation without looking at a volume, but if they are
really hyperintense you may need to manually fill them in in the wm.mgz.
As for mri_cc, you should use aseg.auto_noCCseg.mgz instead of as
Bruce Fischl wrote:
> Hi Judit,
>
> the fornix is labeled in the aseg, not the parcellation, although this
> is not the default). If you rerun mri_cc with the -fornix option it
> will write a volume named mri/fornix.mgz with the fornix in it.
>
> cheers,
> Bruce
>
> On Wed, 1 Jul 2009, Judit Haas
