External Email - Use Caution 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 https://secure-web.cisco.com/1jL9MUfd9oLXR_SVyZl8-wPztrX70T9SJxxJaJElRv5e-Dj4sp4RQ3M4KUFAgUKpZxTsy39_ZpJl8bnnPbnvx2YzJvRH_uTKNfjANjJd-5gjcRF6xLXUfsXjqCmSKGe2yz1c7u_wmpF_bHrEno5pHCvh7SC8bm74VtmPYYNj-YuJSnlcZ85bx_0q82bTlL56VDSPkTK1ifobJsYiFQf7k5pSOsiAvHKbOmRIQvzx-ezp9lvzhHLbD0MIodNOc9hyrNxaG0ZWxK49VfLdGXKCgmg/https%3A%2F%2Fimgur.com%2Fa%2FwrY0HTY 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
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