Hi Nick - This likely means that it got stuck at the initial path for a while,
but eventually got unstuck and explored the space successfully. If you don't
like this look, you can try setting the nburnin parameter in the config file,
to something higher than the default 200. This sets the number of perturbations
of the path that occur in the very beginning, and are then discarded.
Hope this helps,
a.y
On Jan 4, 2019 5:01 PM, Nick Vogt <nv...@wisc.edu> wrote:
External Email - Use Caution
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
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