Hello everyone,
I was hoping someone with experience in susceptibility imaging, especially susceptibility tensor imaging (STI), might be able to help me understand what is happening in my data.
We acquired multi-orientation GRE data with 6 orientations using the following parameters: TE1 / deltaTE / TE6 = 3 / 4 / 23 ms, with TR = 27 ms, and flip angle of 12 degrees.
When I reconstruct QSM for each individual orientation, the maps look good. However, the problem appears when I try to estimate the susceptibility tensor elements.
My processing pipeline is the following:
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ROMEO for phase unwrapping
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VSHARP for background field removal
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Coregistration of all local field maps to the straight-head position
After that, I use an asymmetric STI method to estimate the tensor.
The issue is that when I visualize the χ33 tensor element, I would normally expect something that resembles a QSM map. Instead, what I get looks much more like a local field map.
So I was wondering whether anyone has seen this before, or has any idea what could cause it. Could this be related to:
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a data acquisition issue,
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an error in preprocessing or coregistration,
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a problem with the STI fitting/model itself,
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or something else entirely?
I attached a screenshot showing how the χ33 element looks.
Any suggestions would be greatly appreciated.
Thank you.