Hello Everyone, I just face a problem while deal with the voxel index to position, base on the command [mrinfo] -transform: the transformation from image coordinates [mm] to scanner / real world coordinates [mm]. so I follow the equation : (x, y, z )T = transform_R * (i, j ,k)T + transform_T, where (x, y, z ) stand for the position and (i,j,k) stand for voxel index, transform_R and transform_T all from transform, but the result I calculate can’t fix with the result in mrtrix. Please correct me if I understand something wrong, or any other convenient way to get the position.

thanks a lot!

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The relevant documentation can be found at Images and other data — MRtrix 3.0 documentation.

What I think is missing in your equation is the voxel size, as explained in this excerpt from the page linked above:

In

MRtrix3, the transform shown always corresponds to the transformation from image coordinatesin millimetersto scanner coordinatesin millimeters- the voxel size is not taken into account, and the image axes are always normalised to unit amplitude. This may differ from other packages.

Sorry for taking so long to reply to you, your suggestions have helped me a lot, thank you.

Thank you for your suggestion, this wiki is very helpful!