Dear all,
I'm currently working on a DWI dataset with 100 subjects. The same MRI scanner, acquisition protocol and file format conversion was used. Somehow 15 out of 100 4D nifti images show the coronal and sagittal views upside down. I checked some anatomical landmarks and left-right orientation is correct. I tried to use fslswapdim with x y -z flags but there's one problem: fslview now shows the right part of the brain in the right side of the screen (not in the radiological orientation). I have 4 questions:
1 - Is it ok to use these files together with files in radiological orientation? (it seems obvious to me that it isn't but I'm not an expert)
2 - If it is not ok, how can I correct the z orientation while preserving the radiological orientation?
3 - How can I adjust the bvectors?
4 - How can I prevent this from happening again? I couldn't find any pattern in the occurrence of this over the 100 subjects.
Thank you all in advance,
Best regards.
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