I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that.

NIH

On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration.

a.y

On Mon, 25 Mar 2013, Susan Kuo wrote:

Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject
brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts.
I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration.
However, I am reproducing the same results. Does anybody have an idea why I would see these "spotty" tracts?

Thank you for all your help!

--
Susie Kuo
NIH

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