NIfTI DICOM conversion is changing the original orientation

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Dear Neurostars members,

We have a DICOM series of 336 x 336 having 284 slices. We are using dcm2niix to convert DICOM to NIfTI (LPS to RAS) file and getting the shape of 284 x 336 x 336. When we tried converting NIfTI file back to a DICOM series, it was converted into a series, but the orientation was not matching with the original DICOM. We tried swapping the axis and also tried rotating 90 deg to match the DICOM series, but still getting same orientation.

Could you please advise me on how to resolve this problem?

Thanks in advance.

Best Regards,
Sunita

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Hi, Sunita-

Indeed, that does happen by default. From this thread, I believe that by adding the options -x i -y n, the output NIFTI orientation should still match the input DICOM orientation.

Does that work?

–pt