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
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
External Email - Use Caution
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?
Sent from Mailhttps://go.microsoft.com/fwlink/?LinkId=550986 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
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
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?
Sent from Mailhttps://go.microsoft.com/fwlink/?LinkId=550986 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
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 Mailhttps://go.microsoft.com/fwlink/?LinkId=550986 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
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?
Sent from Mailhttps://go.microsoft.com/fwlink/?LinkId=550986 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
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 Mailhttps://go.microsoft.com/fwlink/?LinkId=550986 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
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?
Sent from Mailhttps://go.microsoft.com/fwlink/?LinkId=550986 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
freesurfer@nmr.mgh.harvard.edu
-
Adam Rytina -
Yendiki, Anastasia