Dear FSL experts:
Although this has been posted on the forum, after reviewing the archives I am still not very sure as to the correct way to extrac each subject's FA value from a certain fiber tract, say left uncinate fasciculus (UF). Below is what I have tried:
1. In fslview, created a ROI in left UF on mean_FA_skeleton and saved as ROI_LUF
2. Used this command (fslmeants -i all_FA_skeletonised -m ROI_LUF -o output_subjectFA.txt) to otain the FA values
However, with this approach, the FA values were nearly 0. I am wondering if this has something to do with the minimum threshold I set for the ROI (if so, what would be thre reasonable min threshold?) or some steps I missed out.
Also, I noticed that when using JHU ICBM-DTI-B1 white matter label to chosse only left-side UF as the ROI, both side UF would be highlighted in fslview. Is it supposed to be like this?
Any clarification/ pointers are highly appreciated.
Best,
wen
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