Shell scripts for AIR 2.0
Why use shell scripts
The alignlinear is at the core of the AIR package. In AIR 2.0, the number
of options associated with this programs makes it difficult to use. Shell
scripts offer an easy way to decrease the number of options associated with
this program and to create multiple version, each tailored to a particular
familiar use.
Modifying and configuring the shell scripts
to work properly
Several sample shell scripts are distributed with the AIR 2.0 package.
They have names of the form align*.com where * is a wildcard.
These are Bourne shell scripts. If typing /bin/sh does not
invoke a Bourne shell on your system (Use control-D to revert to your previous
shell), you must replace /bin/sh in each of these shell scripts to provide
a path that will invoke a Bourne shell before you can execute them.
Each of the scripts contains a line of the form:
MANDATORY=' flags '
where flags are acceptable flags for the program alignlinear that specify
certain behaviors such as setting thresholds, etc. By changing the flags,
you can create tailored versions of alignlinear to perform certain types
of registration.
In order to use a shell script, you must make it executable. For example
to make alignmritopet.com executable, type
chmod +x alignmritopet.com
The scripts must be located in the same directory as alignlinear in order
to work properly.
Modified: January 7, 1996
© 1995-96 Roger P. Woods, M.D.(rwoods@ucla.edu)