Dear FSL experts,
I am trying to track the Pyramidal Tract in healhty
subjects, and found fibers escaping the brain as well as
fibers in areas with very low FA values. Going through
several discussions in the FSL archive, I surmised that
the best way to get rid of these unwanted fibers would be
a Freesurfer-generated white matter mask to be used as
nodif_brain_mask. Consequently, I generated a few white
matter masks with Freesurfer and found that these masks
were not only in a different space, but also has a
different x-y-z orientation from the normalized dti_FA.
What steps are necessary to turn the Freesurfer output
into a FSL-FDT compatible white matter mask?
Thank you very much for in advance. Your help will be
greatly appreciated.
Best,
Theodor
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