I find the T2w image works well for removing dura and blood vessels, but
I'm not sure FLAIR would work for T1w/T2w myelin mapping because of what
would happen to the ratio near the pial surface.
Instructions for T1w/T2w myelin mapping are available here:
http://brainvis.wustl.edu/wiki/index.php/Ca
1a) You would do this after running recon-all on the T1-weighted image. It
will only adjust the surfaces, not the segmentation. Something like
recon-all -T2pial
1b) this will work with either, but in my experience the FLAIR helps more
to distinguish dura from gm
2) Yes. The standard aseg wi
Hi FreeSurfer experts!
We have isotropic T1/T2 and FLAIR volumes for a larger cohort. It would be
fine to use the T2 / FLAIR volumes to improve the segmentation and to
perform a couple additional analyses using FS. This leads to the following
questions:
1) How do I incorporate T2/Flair volumes
