Re: [Freesurfer] how to shrink WM surface in one region

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Hi Bruce,

Thanks for the quick reply. I'm unable to connect to the ftp or file drop sites outlined here: https://secure-web.cisco.com/1J6xj9uOYT0-orYt6Ug7tMaMV01I_XctGV48pcqQv9Tr9ub.... I can log into the ftp server, but don't have permissions access to drop files there.

...So instead, I put the image snapshots in a public google doc here: https://secure-web.cisco.com/183XTP5FLjT6Xx2SHQPem_2YqmbLW8bRZYSzfF6XOXFaE26... Hopefully that will suffice.

Thanks again, Lara

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@mgh.harvard.edu Sent: Wednesday, June 23, 2021 4:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] how to shrink WM surface in one region

Hi Lara

Can you send us some pictures? The answer depends on why the white matter surface is settling at the wrong place Bruce

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Lara Foland-Ross Sent: Wednesday, June 23, 2021 7:11 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] how to shrink WM surface in one region

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Hi everyone,

Very quick question - I need to shrink the white matter surface in a very specific (constrained) region. Can you please confirm that the right way to go about this is to (1) manually remove voxels from the WM volume in freeview, then (2) save edits on that WM volume, and then (3) run recon-all?

Specifically, re: #3 - many brains also need control points, so I'm running " recon-all -autorecon2-cp -autorecon3"

Using this command structure, I'm not seeing that any of the edits I'm making to the WM volume are influencing the white matter surface line... Only the control points.

Thank you in advance, Lara

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