Dear FS developers,

I have run FS’s recon-all on many cases, with and without -FLAIR options. I found the pial  surface results (?h.pial) I obtained without -FLAIR option fit to the original image (subjected/mri/orig.mgz) much better than those with -FLAIR option, at least from my visual judgment. See MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://imgur.com/a/wrY0HTY for one example.

I know -FLAIR option was introduced to improve the quality of pial surface segmentation. Now for many cases, my intuition is that -FLAIR option decreases the pial quality. My questions are:

• Is this intuition correct?
• Should I trust the pial surface that’s obtained with or without -FLAIR option in general?

In addition, when I use the -FLAIR option, I sometimes get failed when running recon-all. After I did some manual edits to the brainmask image, and re-run the recon-all:

recon-all -autorecon-pial -subjid <subjectID>

I can get recon-all successful. But if I run recon-all without -FLAIR option, I can get successful results without needing to manually edit the brainmask image.

So my last question is:

• Should I just run recon-all without -FLAIR option, or, with -FLAIR option + manual edit + re-run with -autorecon-pial? Which is better?

Thank you very much!

John