I got a "WARNING: Unable to determine slice direction: please check whether slices are flipped" in converting Symbia Tomo Recon SPECT image.  What is expected correct orientations when the image is display in MRICron?

My understanding is DICOM slice and slice-wise direction can be determined from the
three values of the Image Position (Patient) (0020,0032) attribute.  If the sign of the first two values are reversed in NIfTI qoffset then could I confirmed that the conversion is correct?

Thanks & Regards,
Marco

You will get this error for 2D slices. The issue is that DICOM is specific about orientation of the slice, but due to the implementation of different vendors it can be ambiguous regarding the depth direction (essentially, a 2D slice does not have a depth) and slice thickness (see links here http://stackoverflow.com/questions/14930...). For this reason, conversion tools compare the values of successive 2D slices when building a 3D stack to ensure precise calculations. This is usually not a problem for brain imaging as 3D acquisitions are required for accurate motion correction and normalization. I suspect you are seeing this message for your scout scan or your unreconstructed data (which for SPECT would be cylindrical). 

In any case, you can always check these results by opening an image with SPM or MRIcroGL and making sure the L->R, A->P and S->I dimensions are correct.