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!

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.