Extrinsic Coordinate Systems

The NIfTI header format includes optional storage for two different coordinate system transformations. When neither of these coordinate tranformation are specified, a third default coordinate transformation is defined using the non-optional voxel sizes (which must be positive to comply with the NIfTI format specification). For any given NIfTI format file, MultiTracer provides direct access to only one of the three transformations. Specifically MultiTracer uses the first available coordinate system from the following priority list:

1. the NIfTI s-form transformation, a potentially affine transformation, typically (but not necessarily) to some standard space
2. the NIfTI q-form transformation, a rigid-body transformation, typically (but not necessarily) to scanner space
3. the default transformation, a simple scaling of voxel index coordinates (referred to in NIfTI documentation as i,j and k) to account for positive voxel size and therefore referred to here as the intrinsic coordinate system (exported UCF files are always reported in this intrinsic coordinate system)

For s-form and q-form transformations, the NIfTI header format also specifies codes designed to identify the extrinsic space targeted by the transformation. MultiTracer identifies extrinsic spaces as follows:

• undefined (this indicates use of the default intrinsic coordinant system when no s-form or q-form transformation is provided)
• Scanner (should be a coordinate system associated with the scanner)
• Aligned (presumably aligned to some target known to the user)
• Talairach
• MNI152

Analyze 7.5 format files do not have s-form or q-form transformations, and MultiTracer uses the default intrinsic NIfTI transformation described above for Analyze 7.5 format files. If the Analyze 7.5 format file has negative voxel sizes, MultiTracer ignores the negative part, taking the absolute value of the size specified in the header. The Analyze 'hist.orient' field is ignored by MultiTracer.

MultiTracer displays the transformed coordinates of the current mouse location in the lower left corner of the main display window with the identity of the extrinsic space following the coordinates in parentheses. Since different files may specify different transformations, placing the mouse at homologous locations in different files may result in different coordinates being displayed.

To save a .air file linking the default intrinsic coordinate system (which is the coordinate space used for exported UCF files) to the preferred extrinsic coordinate system associated with a given loaded file, choose "Save AIR File of Number" with the appropriate slot number (1-16) from the "File" menu. The extrinsic coordinate system name (or intrinsic system if no extrinsic system is identified) will be the 'standard file' in the resulting .air file. The AIR program reslice_ucf can then be used to map contours exported as UCFs into this coordinate system.

Modified: August 28, 2012