[Freesurfer] Noise reduction + Eddy current reduction

2020-01-10 Thread Adam Rytina 
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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Re: [Freesurfer] Noise reduction + Eddy current reduction

2020-01-10 Thread Greve, Douglas N.,Ph.D. 
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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Re: [Freesurfer] Noise reduction + Eddy current reduction

2020-01-11 Thread Adam Rytina 
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-boun...@nmr.mgh.harvard.edu 
 za uživatele Greve, Douglas N.,Ph.D. 

Odesláno: sobota 11. ledna 2020 0:03
Komu: 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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Re: [Freesurfer] Noise reduction + Eddy current reduction

2020-01-11 Thread Greve, Douglas N.,Ph.D. 
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 za uživatele Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Odesláno: sobota 11. ledna 2020 0:03
Komu: freesurfer@nmr.mgh.harvard.edu<mailto: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:

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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Re: [Freesurfer] Noise reduction + Eddy current reduction

2020-01-11 Thread Glasser, Matthew 
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In general these days the more recent “eddy” tool is preferred for eddy current 
correction of diffusion data.

Matt.

From:  on behalf of "Greve, Douglas 
N.,Ph.D." 
Reply-To: Freesurfer support list 
Date: Saturday, January 11, 2020 at 2:54 PM
To: "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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 za uživatele Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Odesláno: sobota 11. ledna 2020 0:03
Komu: freesurfer@nmr.mgh.harvard.edu<mailto: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:

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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