Just as an FYI, we also recently encountered the same problem, also using mri_convert as our DICOM to NIFTI converter. Our work-around was to just switch to dcm2nii.

Jolinda: I don't know why mri_convert is populating a "slice_code" entry for a Siemens MPRAGE acquisition, since an MPRAGE is a 3D acquisition in k-space and it doesn't have a "slice timing pattern".

That said, since the entry is irrelevant for an MPRAGE, and I agree that it shouldn't cause FS to abend.

cheers, -MH

On Thu, 2011-06-16 at 21:56 -0700, Louie Perkins wrote:

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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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