Dear Experts,
I've been working on cleaning up some 4T nifti images for cortical thickness analysis. Initially our images were quite dark inferiorly due to the nature of the RF coil used (it doesn't extend much further than the temples resulting in signal drop-off).
I've managed to find what appears to be a decent fix for the problem by running a higher number of -nuiterations during -autorecon1; usually 20-50 does the trick. Because I'm quite new to this, I was wondering if this is an acceptable fix? Just wanted to double-check with the experts before moving forward.
I've attached a screenshot contrasting image quality of default iterations, 10, 20, and 50 iterations.
It's also worth mentioning that -surfs appear to be quite accurate especially after I lay down some control points after an initial autorecon2 run.
Thank you very much for your help and patience,
Dan
