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-
- 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?
- 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