FSL(fsleyes) displays image space issues (spec2nii GE MRSI)

MRS Software FSL-MRS
1

I am a PhD student in neurosurgery, currently using FSL to process magnetic resonance spectral data. I used spec2nii to convert P-files to NIFTI format and then processed them with FSL-MRS, but the results were completely unreliable. Then, I opened the T2 sequence and spectral data with FSLEYES and found that the image orientation was incorrect; I’m unsure if this is the cause.

I hope someone can help me figure out where the problem is.

Below are the results and detailed information after opening the file using FSLEYES.

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image691×420 55 KB

image
image692×734 72.5 KB

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image692×1020 98.5 KB

image
image692×421 56.3 KB

image
image692×983 46.6 KB

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image682×1163 46.9 KB

2

Hi @doctorjia,

Sorry that this didn’t work out of the box. Could you tell us a bit more about the sequence and what you expect to see? What should the orientation be? Is the data reconstructed? I can see some signal right at the centre of the slice in a checkerboard pattern
image
What does the spectrum look like there?