GDC for Siemens Syngo XA60

[Yash Patel]

Hello HCP experts,

We recently upgraded our Siemens Prisma scanner to Syngo XA60 software and noticed that gradient distortion correction (GDC) is automatically applied to T1w, T2w, and Spin Echo field map images (ImageType: "DIS2D" or "DIS3D"), but NOT to fMRI EPI timeseries (ImageTypeText: "ND"). 
The Issue: HCP pipelines use a single --gdcoeffs parameter for all modalities. Setting --gdcoeffs=NONE avoids double-correction of T1/T2/SpinEcho but also skips GDC for fMRI EPI (which needs it).
Questions:

1. Has anyone else encountered this with Syngo XA60 or similar scanner software?
2. Is there an existing solution or recommended approach for handling pre-corrected images?
3. Any concerns with selectively skipping GDC in PreFreeSurfer/Topup while keeping it for fMRI volume processing?

I've identified that GDC is called separately in PreFreeSurferPipeline.sh, TopupPreprocessingAll.sh, and GenericfMRIVolumeProcessingPipeline.sh, so I can branch/modify the scripts to conditionally skip GDC for T1/T2/SpinEcho when DIS3D is detected, but wanted to check if others have already solved this or have better approaches.
Note: Disabling GDC at the scanner level also disables Intensity Normalization which we want to keep.
Thanks for any insights!

Regards,

Yash

[Glasser, Matthew]

You should be able to configure all of that in your MRI protocol.  Gradient distortion correction doesn’t cause huge changes, but you do want it to be consistent across scans.  We often for research studies have it all set to off and use the HCP Pipelines.  For clinical studies we often have it all on.

Matt.

 

From: 'Yash Patel' via HCP-Users <hcp-...@humanconnectome.org>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, January 28, 2026 at 1:59 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] GDC for Siemens Syngo XA60

 

Hello HCP experts,

We recently upgraded our Siemens Prisma scanner to Syngo XA60 software and noticed that gradient distortion correction (GDC) is automatically applied to T1w, T2w, and Spin Echo field map images (ImageType: "DIS2D" or "DIS3D"), but NOT to fMRI EPI timeseries (ImageTypeText: "ND"). 
The Issue: HCP pipelines use a single --gdcoeffs parameter for all modalities. Setting --gdcoeffs=NONE avoids double-correction of T1/T2/SpinEcho but also skips GDC for fMRI EPI (which needs it).
Questions:

1.      Has anyone else encountered this with Syngo XA60 or similar scanner software?

2.      Is there an existing solution or recommended approach for handling pre-corrected images?

3.      Any concerns with selectively skipping GDC in PreFreeSurfer/Topup while keeping it for fMRI volume processing?

I've identified that GDC is called separately in PreFreeSurferPipeline.sh, TopupPreprocessingAll.sh, and GenericfMRIVolumeProcessingPipeline.sh, so I can branch/modify the scripts to conditionally skip GDC for T1/T2/SpinEcho when DIS3D is detected, but wanted to check if others have already solved this or have better approaches.
Note: Disabling GDC at the scanner level also disables Intensity Normalization which we want to keep.
Thanks for any insights!

 

Regards,

Yash

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[Harms, Michael]

 

Yes, this is known change in the behavior (particularly, the allowed options) in various Siemens product sequences, starting with XA more generally.

 

Hopefully, in the scans in which you used the on-scanner correction, you made sure to specify the 3D (rather than the 2D) version?

 

IIUC, part of the issue here is that if you want to use Prescan Normalize, you can't turn off GDC on the SEFMs??  (If so, is that true for the CMRR MB sequences, or just in SEFMs implemented with the product Siemens SE sequence?)

 

No, we have not implemented a work-around for your specific situation (i.e., GDC already applied on the scanner for the SEFMs, but not the BOLDs). 

 

Matt would have to comment on whether he is willing to accept a PR that implements functionality to not apply GDC to the SEFM processing (because already done on the scanner), but still allows one to apply it to the BOLD (because not done on the scanner).

 

Conceptually, seems mostly like just the addition of another flag, and some minor code changes to make use of that flag.

 

Cheers,

-MH

 

 

-- 

Michael Harms, Ph.D.

-----------------------------------------------------------

Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.

St. Louis, MO  63110

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/C9A41545-FA5A-48FD-BD13-DD80211080B3%40wustl.edu.

[Glasser, Matthew]

I’m happy to accept tested PRs that help users use the HCP Pipelines with emerging data issues. 

 

I’ll note that if you want to use on-scanner static field correction you currently cannot use 3D gradient distortion correction (or you will get severe artifacts).  This is a rare usecase in research, but is a clinically important usecase.

Matt.

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/99D8B067-63E8-4835-8CC4-793B76AD77D4%40wustl.edu.

[Yash Patel]

Apologies for the delay, we are working with Siemens, so I waited to reply with something concrete.

Yes, we made sure to choose 3D Distortion Correction. 

We can turn off GDC for SEFMs and EPIs, just not the T1w/T2w images. It seems like we have 3 variants of data.
1. GDC on without prescan normalization
2. GDC on with prescan normalization

3. GDC off without prescan normalization

It seems that GDC can't be turned off if using the Set N-Go protocol which is standard, we are still working with Siemens to test closing Set-N-Go to acquire the T1w and T2w anat images. The main reason we choose to test is that we prefer the Prescan Normalized images for these two images however currently the Prescan Normalization doesn't work if GDC is turned off. In the previous software i.e. Syngo MR E11 we had all sequences set to GDC off while getting the prescan norm'd images meanwhile now T1w and T2w have them on by default. GDC for EPI sequences and SEFMs can be turned off. 

Also, the other thing I noticed is that our scan tech could reconstruct the T1w and T2w image without the GDC but that reconstructed images still didn't have a prescan norm. Furthermore, considering that it was derived and resampled it was smoother than the GDC T1w/T2w image without prescan norm.

I have worked on and dry tested individual GDCing; by the end of this week, I will have a confirmed subject test run. I will then submit a pull request with this functionality.

Regards,

Yash

[Yash Patel]

I dry tested this functionality with echo statements and will submit a PR once I have a successful run on actual subject data. Thank you!

Regards,

Yash

[Harms, Michael]

 

Hi,

I’m not following why exactly you are having an issue with the EPI scans (BOLD and SEFMs).

 

First, which sequences are you using for both of those?  Siemens product sequences, or the CMRR sequences?

So, if you have the Distortion Correction filter set to Off in the BOLD/SEFM scans, you're saying that the UI doesn't then give you the option to turn On the Prescan Normalize filter?

 

-- 

Michael Harms, Ph.D.

-----------------------------------------------------------

Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.

St. Louis, MO  63110

 

From: 'Yash Patel' via HCP-Users <hcp-...@humanconnectome.org>

Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Monday, February 2, 2026 at 3:26 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "Harms, Michael" <mha...@wustl.edu>

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/b066d04f-e1ed-4851-8e1e-378ac7ffa1a4n%40humanconnectome.org.