[Freesurfer] N3 kernel decrease

External Email - Use Caution

Hello,

I am working on T1 images from multi-sites. One site in particular is producing T1s that have small to large areas of temporal cortex being excluded from segmentation. It seems that there may be an issue with inhomogeneity of the bias field and subsequent over correction. I have 2 scans from each person and the 2nd scan is worse. The second scan from one subject refuses to finish the freesurfer pipeline. It seems to boom out right before segmentation.

I was told to decrease the bias field correction smoothing kernel but have not found where to do that on the Wiki. How do I add that syntax?

Thanks.

Rebecca