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 list https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-October/020762.h.... I hope I didn't miss something anything.
Thanks! Mojmir
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
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=...
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
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.
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 > >_______________________________________________ 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.
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 > >_______________________________________________ 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.
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 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 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.
Here's another implementation https://github.com/Inria-Visages/Anima-Public/wiki/Denoising-tools#nl-means-.... 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 fischl@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 <
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 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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Falk Lüsebrink -
Mojmír Vinkler