Hi there, thank you for the response.
The images started in as dicoms that have the proper orientation, collected in coronal slices. These dicoms (T2 relaxometry) were imported into matlab, where code was run to estimate T2 relaxation times, and then the relaxation times written to nifti from there. I used a nifti header generated from the dicoms using dcm2nii, and can confirm that the image the header was taken from also had the right orientation. For some reason, when I put the header and the data together, the axis labels are wrong. Is there an obvious point in this process where this problem might have occurred?
at this point, I am not even sure where to be looking.
Thanks
Jessie
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