[ITK] [ITK-users] dicom viewer/nifti discrepancy
Johnson, Hans J
hans-johnson at uiowa.edu
Fri Apr 24 14:47:01 EDT 2015
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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