Dear all,
Sorry for spamming, as I have posted this message about 2 weeks ago, but didn't receive an answer just yet. I probably did something wrong :).
I've been preprocessing, in FS5.3, 3T GE data in controls, obese and diabetes patients and adding the available flair to do the pial refinement as follows:
recon-all -i t1 -s participant -all -FLAIR flair -FLAIRpial
This works excellent for most of the scans. Unfortunately, for some scans adding the flair leads to some interesting refinements, either extending outside of the brain.mgz or going deep into the white matter.
I didn't notice any misregistrations of the flair to the T1 scan when checking the bb-registration. I have added some screenshots and the recon-all.log files. The red lines represent the pial with the flair refinement, and the blue lines the pial without the refinement. As you can see, these interesting segmentations are not there when the flair is no used.
Does anyone know what is going on?
Thanks a lot,
Eelco
