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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