[ITK-users] dicom viewer/nifti discrepancy

[Johnson, Hans J]

I don’t have a definitive answer, but NIFTI internal representation is an RAS system, DICOM & ITK internal representations are LPS.

Perhaps there is a coordinate space incompatibility.

Hans

========================================================================
Hans J. Johnson, Ph.D.,  Associate Professor
Electrical and Computer Engineering (Primary), Biomedical Engineering, Psychiatry
hans-johnson at uiowa.edu<mailto:hans-johnson at uiowa.edu>
(319) 621 7185 (cell)
(319) 384 3538  ECE Phone (Primary)
(319) 353 8587 Psychiatry Phone (Secondary)

4316 Seamans Center
Iowa City, IA 52242

On Apr 24, 2015, at 1:37 PM, Nicholas Tustison <ntustison at gmail.com<mailto:ntustison at gmail.com>> wrote:

Hi all,

I have a set of dicom data that were annotated by clinical
folk.  Specifically, I have slice numbers for each image
volume which indicate a particular feature of interest.  The
problem is that the slice number can either be counted from
the most inferior slice or the most superior slice.  When I
view these dicom image volumes in Osirix or Fiji, the slice
number provided by the viewer corresponds to my clinical
numbers.  However, when I convert to nifti (using dcm2nii or
mriconvert), the index, in ITK terminology, always starts from the
most inferior slice.  At first, I thought it was some dicom tag that
was being read by the viewer to orient the index but, after following
a couple of possibilities, I haven’t found anything.  Has anyone
come across anything like this?

Thanks,
Nick
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