5ttgen and infants data


#1

Hello all,

I wonder whether anyone here has experience using 5ttgen or any other script for reasonable tissue segmentation of T1w or T2w of infants?
I need the segmentation results for Anatomically Constrained Tractography.

Thank you,
Mahmoud


#2

That would depend heavily on how old the infants are. If they’re older than 2 or so, there’s a good chance the default approaches in 5ttgen might work out of the box. But neonates definitely need to be handled differently, due to the very different contrast in the images. In this age range, dedicated packages like DrawEM work much better – but it’ll mean you’ll need to create your 5TT images manually, sidestepping the 5ttgen script altogether – shouldn’t be too difficult once you’ve figured out what’s expected.


#3

Thanks for your response. Yes, the challenge is that the infants are younger than 6-months.


#4

In this age range, dedicated packages like DrawEM work much better – but it’ll mean you’ll need to create your 5TT images manually …

Or you could write a 5ttgen algorithm based on such software and contribute it to MRtrix3 :grin: