We recently ran into an issue with Freesurfer's mri_convert tool where it gives an error of "unsupported slice timing pattern". We have some NIFTI MPRAGE files that have a "slice_code" with a value of NIFTI_SLICE_ALT_INC2 (=5).
Issue arises in utils/mriio.c (line 9549 of rev:stable5), two slice_code possibilities are not included in the if-statement, NIFTI_SLICE_ALT_INC2 and NIFTI_SLICE_ALT_DEC2. These are defined in include/nifti1.h (comment says they were added in 2005), so I'm checking to see if there is a reason they are not allowed, or if this bit of code was just never updated to reflect the latest nifti1.h.
Thanks for any help, -Louie Perkins