Hello,

I am having some issues using dcm2niix to convert my DICOMs to NIFTI files that make me question the handling of orientation information within the file. My viewing tool for both file formats has been Mango. When I view the original DICOM, everything appears to be oriented correctly. Upon conversion, the image is flipped. This is problematic because my flipped image is registered to a template that is correctly oriented, resulting in a flipped and failed registration. However, when I use Mango to save my DICOM as a NIFTI file, the orientation and subsequent registration proceed correctly.

I have a large number of images I would like to process, so dcm2niix is an attractive tool for automatic conversion rather than launching Mango to save images one at a time. Is there any other information I could provide that would help diagnose the issue?

Thank you!

Lindsay