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If you are using the HCP Pipelines, you can do the correction post-hoc easily as long as you have the gradient nonlinearity file for your scanner. It is just an extra flag to include.
I believe (and Mike CCed can confirm) that the gradient nonlinearity file is the same for each scanner of a given model and gradient set.
Depending on software version, on-scanner gradient nonlinearity may be required. Mike may remember these details. Also gradient nonlinearity interacts with pre-scan normalize (on Siemens) depending on software version.
I would use the 3D correction if you do on-scanner.
Historically we did the gradient correction offline when we could because then we controlled the interpolation used (preferring spline to trilinear to reduce blurring).
Newer software versions are now including b0 (AKA EPI, AKA susceptibility) distortion correction of fMRI data. We would still do this offline for a research study, but this is great for clinical data where the analysis software may not be able to do this correction.

Matt.

From: Douglas N. Greve <dgreve@mgh.harvard.edu>
Date: Friday, August 7, 2026 at 2:41 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: siemens distortion correction?

No idea. Depending upon the scanner, it is not always perfect, but it is better than nothing. There is some inevitable resampling and so some blurring, so some people will analyze the uncorrected data then apply the correction to the analysis. For 2D scans, I think they will only do the correction in 2D, which is pretty useless.

On 8/6/2026 1:01 PM, Jason Tourville wrote:

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Hi Doug,

Thanks for the reply. There's a good chance that the data will ultimately be used for a pooled analysis of data acquired across multiple sites at some point. In the relatively recent past, we've used the online-corrected scan without applying post hoc correction. When planning a new study, the staff here at BU warned against using that scan. Do you know why there is pushback on using the online corrected scan?

Best,

Jason

On Mon, Aug 3, 2026 at 11:50 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Hi Jason, it depends on what you are going to use it for. If you have a situation where distortion correction is going to be important at some point (eg, multi site study), then I would probably use the distortion corrected version. It is possible to apply it post hoc, but it is a pain. In the end, I don't think it will make much of a difference.

On 7/28/2026 12:44 PM, Jason Tourville wrote:
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Hi Freesurfer supporters,

When collecting T1-weighted MEMPRAGE for input to FS recon, is it better to use the online distortion corrected RMS volume? Or the RMS volume without correction?

Best,

Jason
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