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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Adam Rytina <adam.rytina@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
 

        External Email - Use Caution        

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.

 

Sent from Mail for Windows 10

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <AYENDIKI@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Adam Rytina <adam.rytina@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
 

        External Email - Use Caution        

Iīm sorry I didnīt specify my data. I didnīt 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?

 

Sent from Mail for Windows 10

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <AYENDIKI@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Adam Rytina <adam.rytina@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
 

        External Email - Use Caution        

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