Phew!
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Michael Sent: Wednesday, June 17, 2020 5:18 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correcting recon-all output (missing parts in pial surface)
External Email - Use Caution Thank you for your quick response. The yellow line is the pial surface.
Best, Michael
Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> schrieb am Mi., 17. Juni 2020, 21:12: Hi Michael
Yes, that should work. Is the surface you are showing below the white or pial? Hopefully the pial (using the color we typically use for the ?h.white). If it is the white then our segmentation needs to be adjusted as well
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Michael Sent: Wednesday, June 17, 2020 8:24 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Correcting recon-all output (missing parts in pial surface)
External Email - Use Caution Hello, I ran recon-all on a post-surgery MRI scan. Because of the resection area FreeSurfer did not include certain parts which should be included. What is the correct way of correcting this?
I thought about editing the wm.mgz file by adding missing white matter using a brush value of 255 and erase white matter with a value of 1. Followed by re-creating the surfaces using:
recon-all -autorecon2-wm -autorecon3 -subjid ... Thank you very much. Best Regards, Michael [fs.png]
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