Here's another implementation https://github.com/Inria-Visages/Anima-Public/wiki/Denoising-tools#nl-means-denoising. We'll be comparing different methods and throw in both your and the newer version and see if there's any significant difference at all.
On Fri, Mar 18, 2016 at 10:38 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > thanks Falk > Bruce > On Fri, 18 Mar 2016, Falk Lüsebrink wrote: > > > > > Hi Bruce, > > > > > > > > I have applied one of his denoising algorithms on my high resolution > > datasets and also got very nice results. I used it on a single subject > only, > > however, this could be beneficial for the upcoming hires pipeline to > account > > for lower SNR. > > > > > > > > You can find his algorithms and publications here: > > > > > > > > > https://sites.google.com/site/pierrickcoupe/softwares/denoising-for-medical > > -imaging/mri-denoising/mri-denoising-software > > > > > > > > Best, > > > > Falk > > > > > > > > Von: Bruce Fischl > > Gesendet: Freitag, 18. März 2016 19:43 > > An: Freesurfer support list > > Betreff: Re: [Freesurfer] Replacing / turning off denoising filter > > > > > > > > that's interesting. Is it open source? If so, can you point us at it? > Maybe > > someone should compare it to the version I wrote 20 years ago :) > > > > On Fri, 18 Mar 2016, Mojmír Vinkler wrote: > > > > > Thanks! > > > Just FYI - we applied newer version of NLME from Pierrick Coupé before > > > running freesurfer and it greatly improved segmentation results. > > > > > > On Wed, Mar 16, 2016 at 3:47 PM Bruce Fischl < > fis...@nmr.mgh.harvard.edu> > > > wrote: > > > 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=745 > > > > > 732 > > > > > > > > > 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 > > > onmailinglisthttps:// > mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-Octo > > ber/020 > > > 762. > > > > html. I hope I didn't miss something anything. > > > > > > > > Thanks! > > > > Mojmir > > > > > > > >_______________________________________________ > > > 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. > > > > > > > > > > > > >_______________________________________________ > 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. >
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