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
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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.commailto: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.edumailto: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?
[cid:image001.png@01D9330A.883EB200] [cid:image002.png@01D9330A.883EB200][cid:image003.png@01D9330A.883EB200][cid:image004.png@01D9330A.883EB200]
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
