On 6/20/06, Rahul Desikan <rahul@nmr.mgh.harvard.edu> wrote:

Hi Jeff,

With regards to the cortical parcellation and the mislabelling of the
anterior cingulate cortex (rostral anterior cingulate in the parcellation
atlas), we are aware of this as a problem and are in the process of fixing
it as we speak. If you were interested in editing the parcellation labels,
my suggestion would be to first convert the *.aparc.annot file into
individual labels (i.e. *h.rostralanteriorcingulate.label,
*h.corpuscallosum.label ) and edit the individual labels using tksurfer.
You can view the parcellation labels with the curvature visible (Under
View-->Label Style-->choose Outline instead of Filled) to differentiate
cortical areas from non-cortical areas ( i.e. corpus callosum, unknown).

best,

Rahul

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
>

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