converting FSL FAST segmentation into 5ttgen format

Hi all,

Sorry if this is a very simple question, I am an MRtrix newbie!

I have ex-vivo macaque data that I’d like to run ACT on. I was trying to use 5ttgen fsl to get the required file, but the FIRST command is not optimized for macaque data and the function failed while trying to segment out subcortical structures.

I was able to use FAST to get simple GM-WM-CSF segmentations in NIFTI format, which I think will suffice for our current needs. How do I convert these segmentations into 5TT format?

Hello @pmn1113 and welcome!

I have an edited version of the 5ttgen fsl script that does just that, accepting the path to the directory where your FAST segmentations are, and using them instead of re-running FAST. It does expect a specific file prefix though, something that I still have to fix :o

The script will still attempt to perform FIRST on your data, unless you comment out those sections. I think, however, that you do need a subcortical GM segmentation to perform ACT, as some of the logic regarding truncating and including streamlines depends upon this information. Not sure whether tractography would run without it, or if it is advisable. Maybe @rsmith can expand on this.

Cheers,
Nick