Re: [Freesurfer] Replacing / turning off denoising filter

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-...

Best,

Falk

Von: Bruce Fischlmailto:fischl@nmr.mgh.harvard.edu Gesendet: Freitag, 18. März 2016 19:43 An: Freesurfer support listmailto:freesurfer@nmr.mgh.harvard.edu 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 fischl@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=... 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
  on mailinglisthttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-October/020
  762.
  > html. I hope I didn't miss something anything.
  >
  > Thanks!
  > Mojmir
  >
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