Bbregister is affine, not rigid. Affine registration can account for the geometric distortion of EPIs along the phase encode direction (stretching or compression, depending on the polarity), if the target of the registration is an image that does not have that distortion, such as an MPRAGE.

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Antonin Skoch <ansk@ikem.cz>
Sent: Friday, February 7, 2020 5:38 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] DWI EPI correction

 

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Hi, Adam,

while reading this thread, I would like to clarify:

bbregister does rigid body registration, so you could use this tool for registering EPI to structurals, indeed.
But this tool only registers, it does not unwarp the distortions in the EPI images, it leaves images distorted.

For preprocessing of DWI data, I would recommend the "dwipreproc" wrapper script for FSL tools topup and eddy. This is part of mrtrix3 tool:

https://mrtrix.readthedocs.io/en/latest/reference/scripts/dwipreproc.html

Antonin Skoch



I guess there's a 3rd option: you can correct EPI geometric distortions by 
registering the EPI to a structural scan of the same subject. You can do that 
in FS with bbregister, which uses the surfaces from recon-all to align any scan 
to the T1 of the same subject.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Adam Rytina 
<adam.ryt...@outlook.cz>
Sent: Thursday, February 6, 2020 3:37 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] DWI EPI correction

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Yes, I know this option exists in FSL. I was just wondering whether there are 
some possibilities to perform diffusion data correction in Freesurfer, too.



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________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia 
<ayend...@mgh.harvard.edu>
Sent: Thursday, February 6, 2020 9:35:16 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] DWI EPI correction

In that case, you'll want to use the topup tool in FSL.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Adam Rytina 
<adam.ryt...@outlook.cz>
Sent: Thursday, February 6, 2020 3:32 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] DWI EPI correction


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I´m sorry I didn´t specify my data. I didn´t acquire a field map. I have two b0 
volumes with both polarities for a phase gradient. Is it possible to estimate a 
field map from two b0 volumes in Freesurfer? And afterwards apply the fieldmap 
on other b values volumes to correct susceptibility artefacts?



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________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia 
<ayend...@mgh.harvard.edu>
Sent: Thursday, February 6, 2020 9:27:51 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] DWI EPI correction

The answer depends on how you want to correct susceptibility artifacts. Do you 
have a field map, or do you have DWIs acquired with reverse polarities?
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Adam Rytina 
<adam.ryt...@outlook.cz>
Sent: Thursday, February 6, 2020 2:02 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] DWI EPI correction


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Hello all,

I have an input DWI dataset and wanna perform the diffusion data correction (mg 
susceptibility induced distortion correction, geometric correction...). Does 
Freesurfer enable to perform the diffusion correction? Does recon-all include 
this option?

Thanks a lot
Regards
Adam