I was looking through some e-mails that I had saved about thresholding with probtrackx, but I'm still unsure if I'm thresholding my fdt_paths outputs properly so I wanted to double check one last time before committing to my analyses. Any thoughts, concerns, or advice are greatly appreciated.
Here's what I've done:
1) I used two freesurfer gray matter parcellation labels as seeding points in probtrackx for each subject. There is a known connection between these two regions.
2) Now I'm pulling out the average FA and volume of the resulting fdt_paths using these formulas (thanks again to Steve for helping me figure out this one!)
fslmaths fdt_paths -thr 50 -bin -mul dti_FA_str fdt_paths_values
fslstats fdt_paths_values -M -V
So here are my concerns:
1) I've been using 50 as my threshold for each subject (used the default value of 5000 samples for probtrackx). Is this correct? Or should I be customizing this per subject since the volumes of the seeding points vary across subjects? If I should be varying it, what should I be basing my thresholds on for each subject? Any references in support of either method?
2) Should I only be including voxels that have an FA value above a certain threshold? If so, anyone know of a paper that has looked at the normal range of FA values for white matter?
Sorry for the ton of questions lately, I'm just in the last stretch of my dissertation analyses and I want to make sure I'm doing things correctly before moving forward. Thanks so much for all of your help. I really appreciate it!