Issue with NIfTI Image Orientation After DICOM Conversion

[mikebind (Mike Bindschadler)]

If you are using FSL FLIRT, the post below might also be helpful. Slicer and FSL think about transformation matrices and coordinate systems differently, and you can’t just use an FSL transformation matrix in Slicer and expect it to do what you want. It took me a while to figure out the exact relationship between them, but I hope this can be helpful to you:

Importing FSL FLIRT transformation matrices?

Quick Summary It is possible to convert between Slicer registration transform matrices and FSL/FLIRT registration transform matrices. They differ because Slicer transforms describe transformations within RAS space, whereas FLIRT transforms describe transformations between scaled (and sometimes reflected) voxel spaces. Converting between them requires understanding exactly when FLIRT transforms performed a reflection/translation before registration, as well as what other elements of the images …