[Insight-users] itk::PermuteAxesImageFilter: Order indices must not repeat

[Magnotta, Vincent A]

Yves,

It looks like the Transformation matrix is not orthogonal. The OrientImageFilter requires that the matrix defines three orthogonal vectors. I would  recommend not using this filter and deal with the image in Physical space versus voxel space.

Vince

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From: Yves Martelli <ymartelli at cistib.upf.edu<mailto:ymartelli at cistib.upf.edu>>
Date: Thu, 24 Mar 2011 16:37:42 +0100
To: "insight-users at itk.org<mailto:insight-users at itk.org>" <insight-users at itk.org<mailto:insight-users at itk.org>>
Subject: [Insight-users] itk::PermuteAxesImageFilter: Order indices must not repeat

Dear list,
I am trying to reorient an itk::Image using the itk::OrientImageFilter in ITK version 3.20 but I run into the ‘Order indices must not repeat’ error from the itk::PermuteAxesImageFilter used inside the orient filter.
Here is the mhd header of my data:

ObjectType = Image
NDims = 3
BinaryData = True
BinaryDataByteOrderMSB = False
CompressedData = False
TransformMatrix = 0.828301 0.488478 0.274421 -0.533463 0.537852 0.652789 0.171276 -0.687099 0.706088
Offset = -5.73852 -56.2626 -66.4521
CenterOfRotation = 0 0 0
AnatomicalOrientation = RPI
ElementSpacing = 0.964286 0.964286 0.964286
DimSize = 112 112 111
ElementType = MET_FLOAT
ElementDataFile = image.raw

And this is what I am trying to do:

orienter->UseImageDirectionOn();
orienter->SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RAI);
orienter->SetInput( reader->GetOutput() );

Is there a problem with its orientation that makes it incompatible with the permute filter? Are they any limitations in terms of orientations for the orient filter? Or is there an error in the image file?

Best,
Yves

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