Hi there,
I am running a modified version of the “tract of interest” type of FBA studies that have become popular over the last few years (https://doi.org/10.1016/j.cortex.2023.01.006 and https://doi.org/10.1016/j.cortex.2021.02.015 and https://doi.org/10.1111/psyp.13871 to name just a few).
Specifically, I am examining fixel metrics in connections between specific smaller ROIs instead of across the large-scale tracts that are often segmented with TractSeg in the previous studies. I first run tractography on the population template between my ROIs (using waypoints as necessary), and then crop each subject’s FD, logFC and FDC maps to only fixels within those connections then ultimately perform fixelcfestats within these fixels.
I have a question regarding the tckgen FOD cut-off values. I understand that it is recommended to use the same/similar cut-off value in tckgen that is used for the fmls_peak_value in the fod2fixel step (based on: FBA pipeline - quality check for several steps - #2 by ThijsDhollander). For my data, I am using a fmls_peak_value of 0.08. I then use the cut-off value of 0.08 for tracking some of my connections of interest which gives some good results (after playing around with different thresholds, I found this was the best). However, for other connections, the cutoff value 0.08 results in some messy streamlines which is improved if I change this to 0.10.
My question is (and TLDR): Is it feasible to use a tckgen cut-off value of 0.10 for tracking some of the connections, and 0.08 for others, where the fmls_peak_value is 0.08?
Thanks a lot in advance,
Emily