reconcile_air

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

Purpose:

This program will attempt to reconcile discrepancies in a series of .air files that represent all pairwise registrations of a group of image files. Each pair of images only needs to be represented by a single .air file. A new, more internally consistent, set of .air files will be created.

This program requires that .air files be named in a consistent and orderly fashion. Specifically, the names must take the form *A*B* where each asterisk can represent any character strings that are shared in all of the files being reconciled. A and B are character strings that uniquely identify the reslice and standard files.

Usage:

reconcile_air iterations prefix intron suffix output-prefix output-suffix overwrite?(y/n) id1 id2 [...idN]

where the following definitions apply:

iterations

the number of reconciliating iterations to perform

prefix

a prefix that will be common to all of the input .air file names-- use "null" if you don't want a prefix

intron

an internal separator that will be common to all of the input .air file names --use "null" if you don't want an internal separator

suffix

a suffix that will be common to all of the input .air file names --use "null" if you don't want a suffix

output-prefix

a prefix that will be common to all of the output .air file names --use "null" if you don't want an output prefix

output-suffix

a suffix that will be common to all of the output .air file names --use "null" if you don't want an output suffix

overwrite?(y/n)

'y' if you want preexisting output files with the same names as the current output files to be overwritten

id1

unique identifier that appears in between the intron and prefix or suffix

id2

unique identifier that appears in between the intron and prefix or suffix

...idN

additional unique identifiers

Examples:

• This command will cause the program to load the following files:
  • subj1.airsubj2 (and/or subj2.airsubj1)
  • subj1.airsubj3 (and/or subj3.airsubj1)
  • subj1.airsubj4 (and/or subj4.airsubj1)
  • subj2.airsubj3 (and/or subj3.airsubj2)
  • subj2.airsubj4 (and/or subj4.airsubj2)
  • subj3.airsubj4 (and/or subj4.airsubj3)
• If any of the pairs listed is not represented, the program will stop and complain. Ten reconciliation iterations will be run before creating output files with "new" appended at the end of each file name.
• Files subj1.airsubj1new, subj2.airsubj2new, subj3.airsubj3new, and subj4.airsubj4new will also be created, each of which describes an identity transformation.

Comments:

• It is absolutely essential that the reslice file be represented before the standard file in the .air file names.
• Reconciliation is now defined in terms of the matrix logarithm, making the output independent of the ordering of inputs.

Error messages: (alphabetical by case)

iterations must be a non-negative integer

• supply a non-negative integer

See also:

• definecommon_air