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Hi, I am needing some help with control points.

Environment: - FreeSurfer 8.2.0 - Ubuntu 22.04 on WSL2

I am trying to manually edit a subject using control points for intensity normalization.

Workflow:

1. Open the subject in Freeview. 2. Create a new Point Set. 3. Save it as "Control Points" into: SUBJECT/tmp/control.dat 4. Run:

recon-all -s SUBJECT -autorecon2-cp -autorecon3

The recon-all log shows:

mri_normalize -f SUBJECT/tmp/control.dat ...

using control points from file SUBJECT/tmp/control.dat...

However, immediately afterwards it reports:

Reading 0 control points... error: MRI3dGentleNormalize: mean = 0.0, nctrl = 0

The command completes, but the manually placed control points are ignored.

As a verification, I compared the original and edited normalization volumes:

mri_diff original/mri/norm.mgz edited/mri/norm.mgz

Output:

diffcount 0

which indicates that intensity normalization was unchanged.

Am I doing something wrong? Is this the expected behavior in FreeSurfer 8.2, or is there an issue with how Freeview writes control.dat?