[Insight-developers] world coordinates and slice images - nifti problem?

[Richard Beare]

Hi,
I'm not sure if this counts as a bug, and I haven't tracked down the
root of the issue yet, but thought I'd flag it immediately.

This relates to the same data as my past few posts - single slice MR
time series which I'm trying to do preliminary visualization on.

One of my approaches uses the world coordinates as reported by the
TransformIndexToPhysicalPoint method of OrientedImage.

My problem is that even though I declare the image as 3D, it only has
1 slice, and the PhysicalPoints produced by the transformation all
have a z value of 0. If I concatenate two slices together the results
are as I expect. On the surface it looks like it might be a nifti
loading issue

The differences in image information are (interesting one last):

single slice

  RequestedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [256, 256, 1]
  Spacing: [1.25, 1.25, 1]
  Origin: [-160.625, -157.719, 0]
  Direction:
1 0 0
0 1 0
0 0 1

  IndexToPointMatrix:
  1.25 0 0
0 1.25 0
0 0 1

  PointToIndexMatrix:
  0.8 0 0
0 0.8 0
0 0 1

slice pair

  RequestedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [256, 256, 2]
  Spacing: [1.25, 1.25, 5]
  Origin: [-160.625, -157.719, 9.70944]
  Direction:
1 0 0
0 1 0
0 0 1

  IndexToPointMatrix:
  1.25 0 0
0 1.25 0
0 0 5

  PointToIndexMatrix:
  0.8 0 0
0 0.8 0
0 0 0.2


Orthogonal slice
---------------------

  RequestedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [192, 256, 1]
  Spacing: [1.25, 1.25, 1]
  Origin: [-29.0319, -91.3025, 0]
  Direction:
0.479759 0.985709 0
0.8774 -0.168457 0
0 0 1

  IndexToPointMatrix:
  0.599698 1.23214 0
1.09675 -0.210571 0
0 0 1

  PointToIndexMatrix:
  0.142507 0.833862 0
0.742239 -0.405853 0
0 0 1

Orthogonal slice pair
--------------------------
  RequestedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [192, 256, 2]
  Spacing: [1.25, 1.25, 4]
  Origin: [-29.0319, -91.3025, 135.198]
  Direction:
0.47975 0.0179872 -0.877221
0.877385 -0.00307401 0.479777
0.00593328 -0.999833 -0.0172565

  IndexToPointMatrix:
  0.599688 0.0224841 -3.50888
1.09673 -0.00384251 1.91911
0.0074166 -1.24979 -0.069026

  PointToIndexMatrix:
  0.3838 0.701908 0.00474662
0.0143898 -0.00245921 -0.799867
-0.219305 0.119944 -0.00431412