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Dear TRACULA experts,
I’m hoping someone can provide some insight about why I’m having a little trouble with tract reconstruction using the longitudinal TRACULA pipeline.
As background, the analysis contains 75 middle-aged, cognitively-unimpaired subjects with two time points of imaging (T1 and multi-shell DWI) separated by approximately 2 years. The T1 images have been sent through the longitudinal Freesurfer (6.0) pipeline successfully. The multi-shell data is 2x2x2mm and has 3 b-values (6 b=0, 9 x b=500, 18 x b=800, 36 x b=2000). Prior to use in TRACULA, each DWI volume is noise and Gibbs ringing corrected in MRTrix3, then motion and eddy current corrected using ‘eddy’ in FSL.
I then run the longitudinal TRACULA pipeline according to the instructions online, and everything completes, but some of the tract posterior distributions look a little funny. I’m attaching some images of the CST where the right side is good but the left side is weird. In case those don’t make it through, here’s a description: While some tract posterior distributions look like good, smooth distributions, some of the tract distributions have a distinct high-value single-voxel running through them. My understanding is that if a tract just has this single line, it means there was an issue with the path initialization (this also occurs in my dataset occasionally), but what about if a tract has both a semi-decent looking distribution, but also has this single-voxel high probability tract?
Is there a step or an output that I could check to help understand why this is occurring? I’ve checked the DWI to T1 bbregister outputs, and those look honestly pretty good (considering this DWI data is non EPI-distortion corrected using field maps or topup).
For the longitudinal TRACULA pipeline, what’s the best way to check if the control points calculated from trac-all -prior are good? In cross-sectional TRACULA, the control point coordinates are output in diffusion space (which seems easy to check), but in the longitudinal they’re only in MNI or anatorig (which I assume means base template?).
Any ideas? Thanks in advance!
Nick
