I'm not sure what you mean. Usually, one would edit the proper volumes in freeview using the protocol described (eg, setting edited voxels to certain values). One can implement automatic edits as long as one keeps to the protocol.

On 7/30/2024 5:09 PM, Edwards, Vincent wrote:

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Hello Freesurfer team!
We are editing brain scans using T1/T2 mutual information to improve the original image. Are the recon-all flags the same with as they would be when editing using only the T1 images (i.e., recon-all -cp, -pial, -wm), or are there additional flags are needed after editing?

Thank you,

Vincent Edwards
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