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.
- transformation is meant to describe a spatial inversion
- grants permission to overwrite output-ucf-file
- silently omit unmappable points (default is to report error and exit)
- where the following definitions apply:
- name of the 3D .warp file containing the nonlinear transformation
- the name of the input .ucf file
- the name of the output .ucf file to be
reslice_unwarp_ucf mri.warpatlas caudate_atlas.ucf caudate_mri.ucf
- 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
- 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
- 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.
See also: Generic error messages
- 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
Modified: December 16, 2001
© 2001 Roger P. Woods, M.D.(firstname.lastname@example.org)