jip is the name of a stand-alone command-oriented program designed for basic image manipulations functions. This program is something like Matlab, without all the bells and whistles but also with easier syntax and no purchase required. The program can be used interactively by typing "jip" and then entering commands like this:

                                          Syntax: executable

                         unix% jip                                 unix% jip

                         jip > help                                 jip > read input.nii

                                                                        jip > write output.bshort

                                                                        jip > bye

However, a more useful method is to create a series of commands with an editor and then invoke jip by referencing the command file and also passing arguments from the unix/linux command line. Within the command file, each argument is assigned as $1, $2, ...

                          Syntax: executable [command file name] arg1 arg2 arg3 ... arg9

                          command                                          command file "smooth.com"

                          unix% jip smooth.com data 1.5       read $1.nii

                                                                                   smooth-3d $2

                                                                                   write $1-smooth.nii


Joseph B. Mandeville, Athinoula A. Martinos Center for Biomedical Imaging at MGH/MIT/Harvard