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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 pagehttps://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
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:
External Email - Use Caution
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:
- 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
- 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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