The wm.mgz is expected since we added denoising to it; but it does not matter because wm.mgz is essentially a binary mask of WM. The brainmask.mgz is created from T1.mgz. The T1.mgz will be affected by control points, but only if you run it from the beginning. The surfaces are placed on brain.finalsurfs.mgz, so check to make sure that that volume is being correctly influenced by the control points.
On 9/30/2021 6:51 PM, Staci A Board wrote:
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Hello, our lab has been using freesurfer for years, dating back to version 4.3 and recently ran into a problem with a new installation of 7.2. After adding control points in the typical fashion and saving them into the subject’s tmp folder as “control.dat” and running -autorecon2-cp, mri_normalize seems to correctly identify the control points, the correct number, the mean value and the scaling. The subsequent steps complete without failure and brain.mgz is generated with 110 values in the cp spots. However, the subsequent wm.mgz and brainmask.mgz images do not seem to have been affected by the control points (e.g. the control point locations aren’t at a 110 value and the white matter is almost identical). Curious if anyone else has run into the issue? Is there a new workflow in this version of Freesurfer that I’m neglecting?
So far I have tried to create a new control.dat using freeview and copied the old points into that file, and run twice with the same results.
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