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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@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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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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