External Email - Use Caution
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 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-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
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-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
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
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. ________________________________ 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
External Email - Use Caution
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
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-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
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-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
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
Hi,
according to help, bbregister is rigid:
bbregister --help Help
NAME bbregister
SYNOPSIS bbregister --s <subj> --mov <volid> --reg <regfile> \ --<contrast>
DESCRIPTION This program performs within-subject, cross-modal registration using a boundary-based cost function. The registration is constrained to be 6 DOF (rigid). It is required that you have an anatomical scan of the subject that has been analyzed in freesurfer.
And, the distortions due to magnetic fields inhomogeneities are IMHO typically nonlinear, so even using affine registration would not suffice to precisely compensate for the distortion.
Antonin
Od: "Yendiki, Anastasia" AYENDIKI@mgh.harvard.edu Komu: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu, Antonin Skoch ansk@ikem.cz Odesláno: 7.2.2020 23:44 Předmět: Re: [Freesurfer] DWI EPI correction
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.
----------------
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
External Email - Use Caution 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 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-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
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-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
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
Hello both,
thanks a lot for your answer.
Adam
________________________________ Od: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu za uživatele Yendiki, Anastasia AYENDIKI@mgh.harvard.edu Odesláno: pátek 7. února 2020 23:44 Komu: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu; Antonin Skoch ansk@ikem.cz Předmět: Re: [Freesurfer] DWI EPI correction
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. ________________________________ 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
External Email - Use Caution
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
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-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
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-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
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 -
Antonin Skoch -
Yendiki, Anastasia