reslice_unwarp_ucf

• purpose
• usage
• examples
• comments
• error messages
• see also

Purpose:

This program takes a .warp file and uses the spatial transformation that it describes to transform the coordinates listed in a .ucf file. The .ucf file is assumed to refer to locations in the .warp file's standard file. After transformation the output .ucf file will refer to corresponding locations in the .warp file's reslice file.

Usage:

reslice_unwarp_ucf .warp-file ucf-file output-ucf-file [options]

options:

[-i]

transformation is meant to describe a spatial inversion

[-o]

grants permission to overwrite output-ucf-file

[-s]

silently omit unmappable points (default is to report error and exit)

where the following definitions apply:

.warp-file

name of the 3D .warp file containing the nonlinear transformation parameters

ucf-file

the name of the input .ucf file

output-ucf-file

the name of the output .ucf file to be created

Examples:

• Points in the file caudate_atlas.ucf will be mapped as standard file coordinates to reslice file coordinates that will be output in caudate_mri.ucf. The reslice file and standard file are defined in mir.warpatlas, as is the transformation.

Comments:

• It is not an error that reslice_unwarp and reslice_warp_ucf require numerical inversion of the .warp file, whereas reslice_warp and reslice_unwarp_ucf do not. When an image is resliced, it is necessary to start with coordinates in the standard file and identify corresponding coordinates in the reslice file. In contrast, when mapping coordinates that are already explicitly identified in the reslice file into the standard file, the inverse transformation is required.
• Unless you use the -s flag, you will only get output if every point is successfully mapped. Thus the default assures that all output points are valid.
• If the UCF file is a formal UCLA Laboratory of Neuroimaging UCF file, warnings will be printed if the UCF file appears incompatible with the standard file described in the .warp file.
• 2D warps are not supported
• By default, any point that lies in a region of spatial inversion will generate an error (handling of which will be dictated by the -s flag). If the -i flag is used, any point that does not lie in a region of spatial inversion will generate an error.

Error messages: (alphabetical by case)

3D warp files are required

• 2D warps are not supported. The program scan_warp will let you determine whether a .warp file is 2D or 3D.

Expected ____ valid values, found ____

• Different points in the UCF file have differing number of associated values

Unable to parse ____

• check syntax for undefined flags

Unable to parse argument ____, which was expected to begin with a '-'

• check syntax, an argument without a flag is positioned as if were a flag

See also:

• reclice_ucf
• reslice_warp
• reclice_warp_ucf