Hi Oscar,
1. To perform "tbss-like" analysis in the gray matter they are a couple of approaches, please take a look here:
https://github.com/arash-n/GBSS
and
https://www.ncbi.nlm.nih.gov/m/pubmed/29226284/
2. To look at the FA values of different ROI, in my opinion is better to do it in native space. For doing this you could register any atlas you want to each subject and extract the values you are looking for.
I hope this helps.
Best regards,
Manuel
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