combine_warp

purpose
usage
examples
comments
error messages
see also

Purpose:

This program allows .warp files to be combined with affine .air files so that tranformations that would otherwise require data to be repeatedly interpolated can be done instead in a single step. Multiple .warp files cannot be combined with one another and .air files that include perspective transformations cannot be combined with .warp files.

Usage:

combine_warp output overwrite?(y/n) .air-file1 .warp-file .air-file3

where the following definitions apply:

output: the name of the .warp file to be created
overwrite?(y/n): the letter 'y' if you want to allow a preexisting file with the nameoutput to be overwritten
.air-file1: the name of a .air file that has the same standard file as the .warp file you are trying to create. You can also use 'null' if you want the final .warp file to target the same standard file as the specified .warp file.
.warp-file: the name of the .warp file. It must have a standard file that is spatially equivalent to the reslice file of .air_file1 and a reslice file that is spatially equivalent to the standard file of .air_file3
.air-file3: the name of a .air file that has the same reslice file as the .warp file you are trying to create. You can alsouse 'null' if you want the final .warp file to target the same reslice file as the specified .warp file.

Examples:

combine_warp A.warpC n B.airC A.warpB null

If file A.warpC exists,the program will not overwrite it since overwrite permission has not be granted.
If file A.warpC does not already exist, it will be created by combining the other two files. If A.warpB contains parameters for reslicing file A to match file B and B.airC contains parameters for reslicing file B to match file C, the resulting file A.warpC will contain instructions for reslicing file A to match C.

combine_warp A.warpC n null B.warpC A.airB

If file A.warpC exists,the program will not overwrite it since overwrite permission has not be granted.
If file A.warpC does not already exist, it will be created by combining the other two files. If A.airB contains parameters for reslicing file A to match file B and B.warpC contains parameters for reslicing file B to match file C, the resulting file A.warpC will contain instructions for reslicing file A to match C.

combine_warp A.warpD y C.airD B.warpC A.airB

File A.warpD will be created by combining the other three files. If A.airB contains parameters for reslicing file A to match file B and B.warpC contains parameters for reslicing file B to match file C and C.airD contains parameters for reslicing file C to match file D, the resulting file A.warpD will contain instructions for reslicing file A to match D.

Comments:

Used correctly, this program provides a powerful mechanism for aligning images into any arbitrarily chosen space. It can be made particularly effective if combined with the capabilities of invert_air , combine_air, and manualreslice.
Used incorrectly, this program provides a mechanism for creating total chaos. If any link in the chain of .warp files is incorrect and escapes the error detection features built into the program, the resulting .warp file will be nonsense.
It is absolutely critical that the reslice file in each of the existing .air or .warp files be spatially equivalent to the standard file in the .air or .warp file that follows it in the chain. The program checks for such equivalency directly and also tests whether one of the pair can be assumed to be equivalent to the other after interpolation of cubic voxels.
Unlike combine_air, only three files can be combined, and the one in the middle must be the .warp file. Multiple .warp files cannot be combined. Note that by using combine_air first, you can effectively create any lengh chain that includes only a single .warp file.

combine_warp

Purpose:

Usage:

Examples:

Comments:

Error messages: (alphabetical by case)

See also: