[Insight-users] Image Orientation - what to flip and where

[Kornel]

Hi,

 I'm quite new to ITK and DICOM, and I'd like to make sure I understand
things right - they seem quite important.

* Is it true, that while using DICOM files, every image I'm dealing with
comes in a right-hand coordinate system?

* I've learned that the X values grow to the left hand side of the patient,
z goes from toes to head, and y grows to the posterior of the patient. Or
does that depend on the C.7.6.1.1.1 Patient Orientation? I do not think I
understand this concept of Patient Orientation, maybe since I do not have
any DICOM which would include such a tag.

* Now there is a Image Orientation tag in every (?) DICOM file which
contains the direction cosines of the first row and column of the image. It
is a string a\b\c\d\e\f. This means, that the image I'm dealing with is
translated with respect to the patient by a matrix [a b c; d e f; 0 0 0]. So
when I have a Image Orientation equal to 1\0\0\0\1\0 that means I do not
have to rotate/translate anything, since cos(0) = 1.

* Image Position is the position of the centre of the first voxel, in mm
(?). Seems easy. It is negative, at least in the case of the DIOCMs I'm
dealing with, but I think that's nothing unusual. What I do not understand
is what is it relative to? Is this to make sure that I have consecutive
slices in the right position? Could it happen, that SliceA Image Postion is
equal to 10\10\z while SliceB being the next in the sequence has been
shifted and its position is e.g. 11\10\(z + Slice Thickness)? That would be
quite a mess to worry about.

* What is Slice Location? How is it related to the previously mentioned
data? I'm pretty sure it is :)

* Browsing through the archive I've seen this link:
http://www.itk.org/Wiki/Proposals:Orientation#DICOM_LPS_Orientation_-_Lower_Limb_Graphical_ExampleDo
I understand that right, that the nuerosurgeon and radiologists always
have a different perspective? The radiologists sees the right-hand side of
the patient on the left, while the neurosurgeon on the right.         If so,
it is reflected in the Image Orientation tag, isn't it?         That's quite
a responsibility for both the physician and developer, as far as I know
there's enough of symmetry in the human body to cause confusion.

* Last but not least, I'm transferring data from an itk Image to an unsigned
char array, to display that using OpenGL (for now I'm using just a
IntensityWindowingImageFilter). Now, the image appeared upside down. Image
Orientation is 1\0\0\0\1\0. Is this upside down issue due to the fact, that
in my OpenGL app the y values are growing from bottom to top while in the
DICOM file it's the other way round? I'm using temporary glPixelZoom(1, -1)
to 'fix it', but I'd like to make sure it's right. I've been looking at the
QtImageViewer example (from InsightApplications/Auxiliary) but that didn't
clarify much.

Thanks for any hints, it's quite confusing at first glance, all this
positions, orientations, etc, and I think it might be desirable to
understand them 100% right.

Regards,
 Kornel
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