Hi, I had a couple of questions regarding cortical/subcortical segmentation-<br><br>1.&nbsp; In our cortical segmentation we keep getting what look to be inaccurate segmentation of the rostral and caudal acc.&nbsp; It looks some of what should be labeled as one of those two areas is getting labelled corpus callosum or &quot;unlabelled subcortical&quot; instead, sometimes fairly large chunks.&nbsp; Does this indicate any problem earlier in the processing stream, and is there anything that can be done to prevent this?&nbsp; 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?&nbsp; 
<br><br>2.&nbsp; When registering a freesurfer anatomical to Feat output (using reg-feat2anat) the registration seems to be somewhat inaccurate.&nbsp; Registering brainmask.mgz to our example_func using flirt has given us a better registration so far.&nbsp; Since reg-feat2anat seems to use flirt in its registration I was wondering what the difference might be resulting from.&nbsp; 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?&nbsp; <br><br>Thanks,<br>Jeff<br>