Hi Freesurfers:
I am trying to minimize the amount of skull stripping manual edits I need to make on Freesurfer outputs due to remaining dura. I've been trying both: adjusting the watershed parameters and using gcut.
However, I noticed the output with and without gcut for the same participant were not different. So I went to the log file, and when I searched for gcut it says:
" rm -f brainmask.gcuts.mgz
mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz brainmask.gcuts.mgz
INFO: Care must be taken to thoroughly inspect your data when using mri_gcut. In particular, inspect the edges of gm and cerebellum for over-aggressive cutting. Add -segmentation brainmask.gcuts.mgz to the tkmedit command string to view the voxels which gcut has removed.
reading mask... white mean: 107.529232 threshold set to: 107.529232*0.400000=43.011693 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! masking... ** Gcutted brain is much smaller than the mask! ** Using the mask as the output instead!
cp brainmask.auto.mgz brainmask.mgz "
Thus, it does not appear to be using the brainmask with gcut edits. I added the "-segmentation brainmask.gcuts.mgz" to the tkmedit command and got an error basically saying that the file does not exist. This is the case for many of our participants. Why is this occurring? Isn't the purpose of gcut is to make the brainmask smaller (b/c it has less dura in it)?
Also, any other suggestions for reducing remaining dura/skull?
Thanks for any help you can provide, Jacquie
Jacquelynn N. Copeland, M.A. Doctoral Candidate Medical/Clinical Psychology Program Department of Psychology University of Alabama at Birmingham Email:jcopeland@uab.edu