Hi Omer,
there is actually a work-around for this kind of thing. You need to create a central sulcus label in tksurfer:
1. Load the inflated surface with sulc as the "curvature" overlay. 2. Draw a path across the central sulcus near the vertex to prevent the filling (see below) from escaping the sulcus. 3. Click on a point in the central sulcus. 4. Click the "custom fill" button, and do a fill with "last vertex clicked", "up to and including paths" and "up to and including different curvature". 5. Save the resulting label as lh.central_sulcus.label or rh.central_sulcus.label 6. Rerun mris_register using:
set sd=$SUBJECTS_DIR/$subject set ldir=$SUBJECTS_DIR/$subject/label set sdir=$SUBJECTS_DIR/$subject/surf mris_register -l $ldir/lh.central_sulcus $FREESURFER_HOME/lh.destrieux.simple.2009-07-29.gcs S_central...
where ... means the rest of the normal arguments.
cheers Bruce
On Thu, 15 Sep 2011, Omer Tal wrote:
Hey there,
I was excited to find out that Freesurfer has two atlases built in which do cortical parcellation as I am trying to do analysis on the precentral gyrus ROI only. However, when creating a mask showing the pre-central gyrus parcellation, I noticed that in the middle of the gyrus the algorithm fails and skips to the next gyrus over (the post-central gyrus). I added an image showing the failed parecellation (not sure if it shows up).
Is there any solution around this? Is there where I can change parcellation options to maybe help better restrict the automatic algorithm? Or is there an easy way to redirect/train the algorithm?
Thank you very much for any advice and your time,
Omer Tal, M.S.
UCSD Center for Functional MRI