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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