[Camino-users] Re: Coordinate systems

[Philip A Cook]

Hi,

Camino's coordinate system is right handed in that the cross product of +x and +y will be +z.

A good way to check if everything is OK is to use pdview. This will show exactly how track will interpret the image. See here

  http://cmic.cs.ucl.ac.uk/camino//index.php?n=Tutorials.DTI

It can also adjust the scheme file if necessary. pdview is rendered in voxel space, which is assumed to be "LPI" - I always worry about these terms because I'm not sure everyone agrees what they mean. I mean that x increases Left to right, then y increases Posterior to anterior, and then z increases Inferior to superior. The tensors should also be oriented in this space.

In the example at the bottom of the page the monkey brain is acquired with sagittal slices, so the inf-sup in voxel space is left-right in physical space, and hence the corpus callosum is blue instead of the usual red. Seed points will be correctly translated from physical space, and tracts themselves will be converted to physical space before output. Internally, the tracking is done in voxel space, and the tensor orientations need to agree with that.

Basically, if you can load the image in pdview and the lines trace the white matter correctly, then you should be OK. The nifti transformation will translate points (seed points or points on streamlines) to and from physical space.

Beware that scheme files often specify gradients in the magnet space, which can disagree with both the patient orientation and the ordering of the voxels on disk. Chris Rorden's dcm2nii will attempt to align gradients to physical space during conversion from DICOM. He has some sample DWI data on his website that can be used for testing.

Related, the ANTs package (http://stnava.github.io/ANTs/) has a program RebaseTensorImage, which can be used to convert tensor orientation between voxel and physical space.


On Aug 30, 2013, at 1:03 PM, Birkan Tunc wrote:

> Hi,
> 
> Sorry for my ignorance on coordinate systems; I have some basic questions?
> 
> I could not find info about the default coordinate system of Camino. Is it LAS? 
> 
> A more general question: What happens if I use a DWI and scheme files in LPS coordinates for tractography? Do I have to perform any conversion before using resulting fibers, for instance for visualization after vtkstreamlines?
> 
> Thanks a lot