Hi Brian
usually this is fixable by changing some default parameters in recon-all.
You can try this yourself (the intensity bounds used in mri_segment and
mris_make_surfaces - look at the help), or you can upload a subject
to our ftp site and we can recommend some
cheers
Bruce
On Sun, 28 Jul 2019, Brian Biekman wrote:
External Email - Use Caution
To whom it may concern:
I'm dealing with an issue in my subjects' recon-all output where the white
matter
surface extends into the gray matter, especially in the parietal and posterior
temporal
regions. This is caused by the wm.mgz including too much gray matter. This
issue occurs to
some degree in every subject's scans. This can be fixed with extensive wm
volume edits but
since this appears to be a systematic problem, I wanted to find a solution that
could be
applied to every subject, possibly in the recon-all pipeline. I've tried using
an expert
parameters 2 different ways to no avail. I've changed the -wlo values in
mri_segment but it
removes wm voxels in the temporal lobe from the wm.mgz surface. I've tried
adding the
-prune and -gentle flags to mri_normalize but that appears to make the problem
worse. Is
there a better approach to try? If necessary, I can send a subject's recon-all
output.
--
Brian Biekman Graduate Student, University of Houston
Clinical Psychology, Neuropsychology Concentration
Laboratory of Early Experience and Development (LEED)
bdbiek...@uh.edu
brian.biek...@times.uh.edu
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