[ITK] [ITK-users] dicom viewer/nifti discrepancy

[Nicholas Tustison]

Thanks Hans.  I’ll stew over that and see if it gets me anywhere.


> On Apr 24, 2015, at 11:47 AM, Johnson, Hans J <hans-johnson at uiowa.edu> wrote:
> 
> 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
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> 
>> 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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