combine_air

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

Purpose:

Given a .air file for registering file A to file B, and another .air file for registering file B to file C, this program will combine the two to create a .air file that describes the direct transformation of file A to file C.

Usage:

combine_air output overwrite?(y/n) air-file1 air-file2 [... air-file-n]

where the following definitions apply:

output

name of the .air file to create

overwrite?(y/n)

'y' grants permission to overwrite output

air-file1

name of the .air file that targets the final space into which the images should be transformed

air-file2

a .air file that has a standard file that is spatially equivalent to the reslice file in air-file1

air-file-n

additional .air files, each of which has a standard file that is spatially equivalent to the previous .air file's reslice file, ending with the .air file that describes a file in the space that is to be resliced to match the standard space defined by air-file1

Examples:

• If file A.airC already exists, the program will not overwrite the existing file because overwrite permission was not granted (note that you must specify y or n in all cases).
• If file A.airC does not already exist, it will be created by combining the other two .air files. If A.airB 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.airC will contain instructions for reslicing file A to match C.

• If file A.airE already exists, it will be overwritten. The four .air files will be combined to generate a single .air file for reslicing file A to match file E (assuming that the file naming conventions in this example are the same as in the preceding example).

Comments:

• Used correctly, this program provides a powerful mechanism for linearly aligning images into any arbitrarily chosen space. It can be made particularly effective if combined with the capabilities of invert_air and manualreslice.
• Used incorrectly, this program provides a mechanism for creating total chaos. If any link in the chain of .air files is incorrect and escapes the error detection features built into the program, the resulting .air file will be nonsense.
• It is absolutely critical that the reslice file in each of the existing .air files be spatially equivalent to the standard file in the .air 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.
• Note that the program invert_air can be used if you have a reslice parameter file for aligning two files in one direction but you need the inverse transformation for use with this program.
• If you want to combine a .air file with a nonlinear .warp file, use combine_warp

Error messages: (alphabetical by case)

Name of output .air file cannot contain .hdr or .img

• provide a name that does not contain .hdr or .img

See also:

• combine_warp
• invert_air