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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-boun...@nmr.mgh.harvard.edu> on behalf of "Greve, Douglas
N.,Ph.D." <dgr...@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:
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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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
za uživatele Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Odesláno: sobota 11. ledna 2020 0:03
Komu: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto: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
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