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.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.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Michael
Sent: Wednesday, June 17, 2020 8:24 AM
To: 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

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