You can edit the wm.mgz directly; if you are using 7.2, you can edit the
filled.mgz
On 10/8/2021 4:30 PM, Staci A Board wrote:
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Hello,
Thank you for your reply. I went back and checked
the brain.finalsurfs.mgz and it is changing the values to 110 and
looks much better. The aseg.mgz is also looking better after the edits
as well.
When we typically do successive passes through the brain, we usually
compare the wm.mgz and the brainmask.mgz to determine where controls
points need to be added. Since the wm.mgz mask is not being changed
from the control points, which volumes do you suggest we use to see
white matter changes after multiple edits?
Thanks
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Friday, October 8, 2021 9:43 AM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Problem with intensity normalization
control points
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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External Email - Use Caution
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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