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Hi Greve,

thanks for your answer. I will try ANTS DenoiseImage.

Regarding Eddy Current - moreover, i have to reduce the eddy current on DWI images. Does Freesurfer enable to perform the eddy current reduction?

Thanks a lot Regards Adam

________________________________ Od: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu za uživatele Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Odesláno: sobota 11. ledna 2020 0:03 Komu: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Předmět: Re: [Freesurfer] Noise reduction + Eddy current reduction

We don't have anything to denoise. You can try using ANTS DenoiseImage, but using on the input might change where the surface is placed. We are experimenting with using it inside the stream in a place where it is less likely to bias the surface placement.

I don't understand the eddy current question as there should not be eddy currents in a typical T1 or FLAIR

On 1/10/2020 2:53 PM, Adam Rytina wrote:

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Hello all,

I want to apply the denoising and eddy current reduction on input images 3DT1 and 3D Flair. Are there any algorithms in Freesurfer to perform the noise and eddy current reduction? Does recon-all involve denoising and eddy current reduction? If so, in which processing stage?

Thanks a lot Regards Adam

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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In general these days the more recent “eddy” tool is preferred for eddy current correction of diffusion data.

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Saturday, January 11, 2020 at 2:54 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Noise reduction + Eddy current reduction

No, I've always used FSL's eddy_correct On 1/11/2020 2:17 AM, Adam Rytina wrote:

External Email - Use Caution Hi Greve,

thanks for your answer. I will try ANTS DenoiseImage.

Regarding Eddy Current - moreover, i have to reduce the eddy current on DWI images. Does Freesurfer enable to perform the eddy current reduction?

Thanks a lot Regards Adam

________________________________ Od: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu za uživatele Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Odesláno: sobota 11. ledna 2020 0:03 Komu: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Předmět: Re: [Freesurfer] Noise reduction + Eddy current reduction

We don't have anything to denoise. You can try using ANTS DenoiseImage, but using on the input might change where the surface is placed. We are experimenting with using it inside the stream in a place where it is less likely to bias the surface placement.

I don't understand the eddy current question as there should not be eddy currents in a typical T1 or FLAIR On 1/10/2020 2:53 PM, Adam Rytina wrote:

External Email - Use Caution Hello all,

I want to apply the denoising and eddy current reduction on input images 3DT1 and 3D Flair. Are there any algorithms in Freesurfer to perform the noise and eddy current reduction? Does recon-all involve denoising and eddy current reduction? If so, in which processing stage?

Thanks a lot Regards Adam

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