Hi Mojmir
we don't apply mri_nlfilter by default so there is no need to turn it off. You are welcome to try it out. It implement some nonlinear filters including what is now called nonlocal means as described in this paper:
http://ieeexplore.ieee.org/xpl/abstractAuthors.jsp?reload=true&arnumber=...
cheers Bruce
On Wed, 16 Mar 2016, Mojmír Vinkler wrote:
Hi, I was wondering if it's possible to replace or turn off your denoising algorithm `mri_nlfilter`. We'd like to try different denoising filters and compare how they influence segmentation performance. Right now we're applying filter before running recon-all, but I fear that applying your filter on already filtered image might degrade our analysis.
I couldn't find any mention of mri_nlfilter besides this one on mailing listhttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-October/020762. html. I hope I didn't miss something anything.
Thanks! Mojmir