Hello all,
I am new to FreeSurfer and still trying to understand how things work. I am currently trying to understand how the manual correction works.
Following the online tutorials I was able to fix the brainmask and wm.mgz, and also add control points in the wm so that low intensity wm is also included in the segmentation.
In the tutorials it is suggested to run the FreeSurfer after doing the brainmask correction by recon-all -autorecon2 -subjid <subject name>
After the wm control point addition, the tutorial says that "run the program with -autorecon2-cp"
Is it possible to do brainmask correction, white matter edits and control points in one session and run the FreeSurfer again to fix all this at once? Is there a different command for this?
I apologize if this has been answered before.
Thanks a lot. Deniz.
Yes, you would just run the command for the fix that happens earliest on in the processing stream. The order these fixes occur in the processing stream is: control points wm edits pial edits
So if you've done all 3, you only need to run recon-all -autorecon2-cp -autorecon3 -s <subjid>
and it will take care of all those edits for you. Allison
freesurfer@nmr.mgh.harvard.edu
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Allison Stevens -
Deniz Ozgen