[Insight-users] GDCM orientation issue....

[Simon Warfield]

Neil Weisenfeld wrote:

>
> Hi all,
>
> The GDCMImageIO reader seems to take the direction cosine vector for 
> rows and columns and crosses them in order to get the slice direction.
>
> How does this account for the direction of acquisition?
>
> I seem to have two volumes with identical slice orientation (L->R, 
> S->I), but one with slices running A->P and the other with slices 
> running P->A.  Both are assigned the same orientation matrix.
>
> Is it not the case that the progression of ImagePositionPatient from 
> slice to slice is needed to decode a sign for this?
>
My understanding is DICOM guarantees the coordinate system is right 
handed and that the 'unencoded' direction cosine is the cross-product of 
the other two.
This tells you about the axes of the coordinate system.
ftp://medical.nema.org/medical/dicom/2004/printed/04_03pu3.pdf  page 275 
guarantees the coordinate system is right handed.

See also the discussion on Patient Orientation here:
http://www.faqs.org/faqs/medical-image-faq/part2/


There is not an obvious way to determine what constitutes 'consecutive' 
slices or the first and last slices other than from the Image Position 
(Patient) tag. For example, I don't believe you can infer 'consecutive' 
from the file name or part of the file name, or from the 'instance 
number' (a tag with an undefined start value and an undefined ordering 
but which identifies each image).    All I can see you can do is to sort 
the slices based on the Image Position (Patient) tag and this will run 
from the most negative position to the most positive position along the 
Z axis defined by the direction cosines.




> I apologise if I'm adding unnecessarily to the pile.
>
>
>
> Neil
>
>
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-- 
Simon K. Warfield, Ph.D. warfield at bwh.harvard.edu Phone:617-732-7090
http://www.spl.harvard.edu/~warfield           FAX:  617-582-6033
Associate Professor of Radiology,          Harvard Medical School
Director, Computational Radiology Laboratory
Thorn 329, Dept Radiology,  Brigham and Women's Hospital 
75 Francis St, Boston, MA, 02115
MA 280, Dept Radiology, Children's Hospital Phone: 617-355-4566