reslice_warp_ucf 
This program takes a .warp file and attempts to
numerically invert 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 reslice file. After transformation the output .ucf file
will refer to corresponding locations in the .warp file's standard file.
reslice_warp_ucf
.warp-file
ucf-file
output-ucf-file
[options]
- options:
- [-c accuracy]
- specifies accuracy (in voxels) of numerical inversion
- [-i]
- transformation is meant to describe a spatial inversion
- [-l linear-estimate-air-or-warp-file]
- name of linear .air or .warp file used to estimate starting point for numerical 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:
-
- accuracy [-c]
- numerical inversion requires finding a location in the standard file that
maps to a given location (specified by the ucf-file) in the reslice
file. This value specifies, in voxels, how close to the location in the reslice
file the inversion must come
- linear-estimate-air-or-warp-file [-l]
- the name of an affine .air file or first order .warp file that has the same
reslice and standard files as the .warp-file.
This file will be used to estimate a good starting estimate for numerical
inversion
- output-ucf-file [mandatory]
- the name of the output .ucf file to be
created
- .warp-file [mandatory]
- name of the 3D .warp file containing the nonlinear transformation
parameters
- ucf-file [mandatory]
- the name of the input .ucf file
reslice_warp_ucf mri.warpatlas caudate_mri.ucf caudate_atlas.ucf -l mri.airatlas
- Points in the file caudate_mri.ucf will be mapped as reslice file coordinates
to standard file coordinates that will be output in caudate_atlas.ucf. The reslice
file and standard file are defined in mri.warpatlas, as is the transformation. The .air
file mri.airatlas should have the same reslice and standard files as mri.warpatlas and
should describe an affine (non-perspective) linear transformation that is used to seed
the iterative attempt to map points using mri.warpatlas.
- 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 reslice 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.
See also: Generic error messages
- -c must be followed by a positive number
-
- -l must be followed by an affine air file or linear warp file
-
- supply an affine (not perspective) .air file name or first order warp file
name
- 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.(rwoods@ucla.edu)