Hi John

you can try mri_nlfilter if you like. It implement a nonlocal means/medians algorithm that I wrote in 1995 or so:

Bruce Fischl and Eric L. Schwartz. 1999. Adaptive Nonlocal Filtering: A Fast Alternative to Anisotropic Diffusion for Image Enhancement. IEEE Trans. Pattern Anal. Mach. Intell. 21, 1 (January 1999), 42-48. DOI=http://dx.doi.org/10.1109/34.745732

I'm not sure I would trust thickness estimates after nonlinear filtering, but it might help getting surface reconstructions and parcellations and such.

cheers Bruce

On Tue, 21 Jun 2016, John Anderson wrote:

Hi FS experts, I have T1 images with low quality (noise and artifacts). I am wondering if smoothing these images, before runing the command "Recon-all", can help to improve the segmentation and parcellation process for these images. Thanks for any advice! Bests, John