combine_warp

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

Purpose:

Mathematically combines a .warp file with any number of compatible .air files to create a single .warp file that directly achieves the spatial transformation described by sequential application of the .air and .warp files.

Usage:

combine_warp output overwrite?(y/n) [.air-file1....airfileN1] .warp-file [.air-fileN1+1....air-fileN2]

where the following definitions apply:

output

the name of the .warp file to be created

overwrite?(y/n)

'y' grants permission to overwrite output

.air-file1....airfileN1

an optional sequence of .air files with the standard file of each being spatially equivalent to the reslice file of the one before it

.warp-file

the input .warp file, which, if preceded by a .air file, must have a standard file that is spatially equivalent to that .air file's reslice file

.air-fileN1+1....air-fileN2

an optional sequence of .air files, the first of which must have a standard file that is spatially equivalent to the .warp file's reslice file; similarly each subsequent .air file must have a standard file that is spatially equivalent to the preceding .air file's reslice file

Examples:

• If file A.warpC exists,the program will not overwrite it since overwrite permission has not been 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.
• Note usage change from AIR 3.0 where a bogus argument 'null' was required after A.warpB

• 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.
• Note usage change from AIR 3.0 where a bogus argument 'null' was required before A.warpC

• File A.warpG will be created by combining the other six files.
• Note usage change from AIR 3.0 where multiple .air files could not be combined.

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 .air or .warp files is incorrect and escapes the error detection features built into the program, the resulting .warp file will be nonsense.
• Only a single .warp file can be specified, this program does not support combining .warp files with one another
• 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 to cubic voxels.
• Note that the usage of this program is changed from AIR 3.0 and that this may break certain preexisting scripts. The enhanced functionality of the program was felt to justify this change. Scripts can be modified easily to simply remove and bogus 'null' arguments.
• The .air files cannot include perspective transformations. An error will be generated if an attempt is made to use a perspective transformation .air file

Error messages: (alphabetical by case)

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

• provide an output name that does not include .hdr or .img

See also:

• combine_air