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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.