Dear Eli,
did you read my response to your previous thread?
I recommended you to try adding control points to the white matter.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51959.html
Regards,
Antonin
Hello all,
Again, I tried to modify the white matter surface by adding voxels to
the wm.mgz file, and performed the reconstruction by doing the
following.
-Opened brainmask.mgz for reference
-Opened wm.mgz on top of that
-Click the voxel edit button
-Check the recon editing checkbox
-Fill in voxels where I want to extend the whitematter surface
-Save wm.mgz
-At terminal, from the appropriate subject directory, run:
recon-all -autorecon2-wm -autorecon3 -subjid my_subject -sd `pwd`
Once this is finished, I examine the surfaces, but they have not
changed. lh/rh.white should be changed to include the voxels I painted
in, correct?
I have no problem removing voxels from the pial surface, but extending
the white matter is for some reason not working for me, so I am really
stumped as to why these wm.mgz edits aren't making any difference.
Any help with this is vastly appreciated. I have tried this several
times on different subjects with no luck.
Here are links to some relevant files.
001.mgz:
https://1drv.ms/u/s!AoOsIIayCH7qlxLBNvCT4JCvM1Kc
recon-all.logs.tar.gz:
https://1drv.ms/u/s!AoOsIIayCH7qlxRGOWpUCttk5Zji
brainmask+surf+wm.tar.gz
https://1drv.ms/u/s!AoOsIIayCH7qlxbDSS54gfHkq2M3
Thanks,
Eli