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I don’t have a definitive answer, but NIFTI internal representation is an RAS system, DICOM & ITK internal representations are LPS.
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<div class="">Perhaps there is a coordinate space incompatibility.</div>
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<div class="">Hans</div>
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========================================================================<br class="">
Hans J. Johnson, Ph.D., Associate Professor <br class="">
Electrical and Computer Engineering (Primary), Biomedical Engineering, Psychiatry <br class="">
<a href="mailto:hans-johnson@uiowa.edu" class="">hans-johnson@uiowa.edu</a> <br class="">
(319) 621 7185 (cell)<br class="">
(319) 384 3538 ECE Phone (Primary)<br class="">
(319) 353 8587 Psychiatry Phone (Secondary)<br class="">
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4316 Seamans Center<br class="">
Iowa City, IA 52242</div>
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<div class="">On Apr 24, 2015, at 1:37 PM, Nicholas Tustison <<a href="mailto:ntustison@gmail.com" class="">ntustison@gmail.com</a>> wrote:</div>
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<div class="">Hi all,<br class="">
<br class="">
I have a set of dicom data that were annotated by clinical<br class="">
folk. Specifically, I have slice numbers for each image <br class="">
volume which indicate a particular feature of interest. The <br class="">
problem is that the slice number can either be counted from<br class="">
the most inferior slice or the most superior slice. When I<br class="">
view these dicom image volumes in Osirix or Fiji, the slice<br class="">
number provided by the viewer corresponds to my clinical <br class="">
numbers. However, when I convert to nifti (using dcm2nii or <br class="">
mriconvert), the index, in ITK terminology, always starts from the <br class="">
most inferior slice. At first, I thought it was some dicom tag that <br class="">
was being read by the viewer to orient the index but, after following <br class="">
a couple of possibilities, I haven’t found anything. Has anyone<br class="">
come across anything like this?<br class="">
<br class="">
Thanks,<br class="">
Nick<br class="">
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