Sorry, I don't have much to share. Siemens a file on the scanner
computer that holds the spherical harmonics used to do the 3D
correction. Maybe they have one that some how just does the 2D correction.
On 7/18/2025 10:13 AM, Annchen Knodt wrote:
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I have a longitudinal dataset collected on a Siemens Skyra, where
online distortion correction on the T1s was turned OFF for the first
wave several years ago, and with an upgrade to XA30 since then, it is
now turned ON for the second wave of data collection and performing a
2D (in-plane) correction.
Obviously, we want the acquisitions to match as closely as possible
between the two timepoints, so I am trying to figure out how to use
gradunwarp to perform post-hoc correction on the first scans. A
problem I am running into (see my thread on HCP’s gradunwarp github
page
<https://secure-web.cisco.com/1UEsGaoLMJInc49tXx1leDHidHoj0m6ydT6viNz9VH1gN5QK96EOKRRN541rbTGjNB-IR34ImGwyVF4FENAquXT1TN5MqViczebRDZtEm27_BBlol2ITUGILUx-w6p9Nk_XlBaYh3nSnbU5mCgCqMOZ1_NaA5Du9SmWOi7dsOIYQQHkHR9JvWmfaw8VpeXW1qqdE6-Tz_7LHG1Hy-TI-bSIifCQIgzVPda0nIU6tAsd790nIOhnO8YoemEDsrO0O4Fjy2Fte8bUix8EHI0WDC0QRt7p0LUSvaMR2xsXR9Mfq9cFrbUJh9oUSx8kQVPE0f/https%3A%2F%2Fgithub.com%2FWashington-University%2Fgradunwarp%2Fissues%2F21>)
is that the software performs a 3D correction, which is not the same
as the 2D correction being applied to my wave 2 data. I don’t yet
know of a way to either:
1. apply just a 2D correction to my wave 1 uncorrected data to match
what the scanner is doing at wave 2 (I’ve communicated with a
Siemens rep who says there is no documentation he can share on the
2D correction to help me figure out how to do this) or
2. UNDO the 2D correction on my wave 2 data, so that I can then use
gradunwarp to apply the 3D correction to both waves.
I don’t have a very good understanding of the differences between the
2D and 3D corrections, and I do not currently have a dataset with both
uncorrected and 2D-corrected copies of the same scan to allow me to
experiment with and test various strategies (hoping to get this soon,
but not sure when I’ll be able to). As such, I am hoping that someone
with more experience or knowledge on this might be able to shed some
light on the nature of the issue and severity of the problem and/or
offer guidance on how I might be able to correct it.
Thanks!
Annchen
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