Hi Stacey

we recommend processing all of your subjects the same way. Do you understand why some would have a big bias field and some would not? It was always the same coil, wasn't it?

cheers Bruce On Mon, 9 Jul 2018, STACEY M SCHAEFER wrote:

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Hello Freesurfer experts,

Our current 3T T1s exhibit structural hyperintensities due to the inhomogeneity of the receiver coil, but not all scans have hyperintensity issues.  The local MRI physicist suggests running N4BiasFieldCorrection through multiple iterations prior to Freesurfer processing on problematic scans.

We would like your opinion as to whether running a bias correction on the individual problematic scans could introduce any additional biases in Freesurfer processing. This is a longitudinal sample of ~ 300 participants. Is it OK to run N4BiasFieldCorrection on individual scans as needed?  Or would it be better to run the bias correction on all the scans (the entire sample) routinely, even if they do not show hyperintensity issues so all scans are processed similarly across the sample?   Or do you have any other suggestions?

Your guidance is much appreciated! Thank you. Stacey

Stacey M. Schaefer, Ph.D. Center for Healthy Minds

University of Wisconsin-Madison

625 W Washington Ave

Madison WI 53703

608-263-9321