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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
