Hi Paul,

The inferior temporal regions are the trickiest, especially in low quality scans - without seeing any images, you may have achieved as close as you are going to get.

Be careful with control points, more is not always better, quality over quantity, you want to be sure you have put them in correct locations, not on partial volumed voxels, and only in regions that are supposed to be wm.

While adding voxels to the wm volume will have some impact on where the final surface lays, it is also dependant on finding the best intensity gradient. If your scans are lower quality with intensity troubles that will likely trump any edits you've made.

If you'd like to upload one of your subjects I am happy to take a look at it - although I will be out of town all next week so it might take me a while to get to it.

Jenni

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Paul Greenberg Sent: Friday, January 05, 2007 7:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] control points and white matter edits

Hi all,

I'm having trouble getting accurate white and pial surfaces in inferior temporal regions on a few lower quality scans with significant intensity variation. I've added hundreds of control points and drawn in white matter in these regions when control points failed to recover unlabeled cortex, but when re-running the scripts with either -autorecon2-wm, or -autorecon2-cp, followed by -autorecon3 the surfaces are still not accurate. Are there other interventions I can to to get more accurate surfaces? If you manually add white matter why will the regenerated white matter surfaces not always extend around the hand drawn parts?

Thanks, Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer