Hi Dan

if the surfs look good you are all set. Does it go from left to right or 
right to left? Rightmost temporal lobes look the darkest to me. I would 
have thought you would still need some control points, but if not that's 

On Fri, 5 
Apr 2013, Dan LaFreniere wrote:

> 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
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