Hi Again

You need to look through the processing steps and see where things went wrong. Is this a watershed failure? Or a topology fixing one? If watershed you can try mri_synthstrip and see if it fixes your problem. If topology correction you need to figure out where it is getting hung up

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Rakshathi Basavaraju
Sent: Saturday, January 28, 2023 4:20 AM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Fwd: A doubt regarding autorecon after watershedding

External Email - Use Caution

Reposting this question.

Dr. Rakshathi Basavaraju (M.D. Psychiatry)

Assistant Professor (Department of Health Research-sponsored return-home research fellowship)

Principal Investigator - OPCINSS

Department of Psychiatry

National Institute of Mental Health and Neurosciences (NIMHANS)

Bengaluru, Karnataka, India-560029

Phone: +91-9480829898/+91-80-26972156/+91-80-26995320

---------- Forwarded message ---------
From: Rakshathi Basavaraju <rakshathi.b@gmail.com>
Date: Fri, Jan 27, 2023 at 3:46 PM
Subject: A doubt regarding autorecon after watershedding
To: <Freesurfer@nmr.mgh.harvard.edu>

Dear FS,

I intend to examine cortical thickness correlates of negative symptoms in my schizophrenia sample. I ran recon-all and corrected a few brainmasks which were excessively stripped by watershedding with different h values (ran autorecon-pial for those watershedded). I am attaching a few screenshots of scans where the segmentation is erroneous and the aseg omits the right temporal and parietal or cerebellar regions. How do I set this right?