[Insight-users] MR orientation problem

[Taru S]

Hello,

I am new to ITK and need your help with my MR orientation. I have generated
a surface model by segmenting an MR volume generated using ITK from Axial MR
dicom slices.

However, when I view the Axial dicom slices they are not correctly oriented
(please see the attachment). The sagittal and coronal views in the figure
are generated from axial reslicing. As a result of this mis-orientation, the
surface model doesn't appear aligned with the slices.

The direction cosines of my MR dicoms are not orthogonal/identity matrix.
The output after applying these direction cosines to my input dicom
(Resample image filter )set doesn't seem to make any difference.

Using identity matrix in place of the direction cosines yields black images.
I am confused because the images don't appear tilted when viewed using Snap
even with Oblique orientation mode.

I will really appreciate your help in resolving this issue.

Thank you,
Taru

Below is some of the information regarding my input MR dicoms:
"
Input
Image (00000000039FFC80)
  RTTI typeinfo:   class itk::Image<short,3>
 ...
  LargestPossibleRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 70]
  BufferedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 70]
  RequestedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 70]
  Spacing: [0.2734, 0.2734, 1.69992]
  Origin: [-135.322, -47.2921, -102.134]
  Direction:
0.986099 0.164923 -0.0200774
-0.165591 0.965578 -0.200612
-0.0137026 0.201148 0.979465

  IndexToPointMatrix:
  0.269599 0.0450899 -0.03413
-0.0452726 0.263989 -0.341024
-0.00374629 0.0549939 1.66501

  PointToIndexMatrix:
  3.60681 -0.605614 -0.0501069
0.60329 3.53173 0.735726
-0.0118108 -0.118012 0.576182
"
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