glad to hear it On Sat, 6 Apr 2013, Dan LaFreniere wrote:

Hi Bruce,

Apologies for the delay - was having some issues with the automatic moderator approval.

That's good to hear, thank you for your help. You're spot on, the right temporal lobes appear to be in worse shape than the left. Control points certainly help a great deal with these images. The surfs seem pretty good - I've attached a screen of the surfs for you from the same subject and same slice (these are following an -autorecon2-cp run). No major problems from what I can see.

Cheers,

Dan

On Fri, Apr 5, 2013 at 11:09 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: 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 great
  Bruce


  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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