We've been manually editing brainmask.mgz to remove voxels that are included in the pial surface that shouldn't be, and recently found on the wiki that to remove cerebellum voxels we should be editing brain.finalsurfs.manedit.mgz instead. What is the reason for this difference? Do we need to redo edits that we've done only on brainmask.mgz? We are going to be looking at cortical thickness.
Thanks, Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia
Hi Jordan, I just had a similar discussion (off-list) with Nick recently. The distinction only matters if you end up trimming cerebellum voxels out of the aseg, and want your aseg for cerebellum to be correct.
Quoting Nick: "it [brain.finalsurfs.manedit.mgz] is used only in the instance (which has happened only once recently) where the pial surface extends into the cerebellum. in this case, you wouldnt want to trim away the cerebellum in brainmask.mgz, because then the cerebellum segmentation wont be correct in the aseg (or worst case the alignment to the atlas wont not be optimal). so we decided to add editing of brain.finalsurfs.manedit.mgz, since this is downstream of the aseg and is input to surface creation.
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Edits to brainmask.mgz still get applied, and if all you are doing is looking at cortical thickness, then you shouldn't need to do redo anything.
cheers, -MH
On Fri, 2011-11-18 at 11:55 -0800, Jordan Pierce wrote:
We've been manually editing brainmask.mgz to remove voxels that are included in the pial surface that shouldn't be, and recently found on the wiki that to remove cerebellum voxels we should be editing brain.finalsurfs.manedit.mgz instead. What is the reason for this difference? Do we need to redo edits that we've done only on brainmask.mgz? We are going to be looking at cortical thickness.
Thanks,
Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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