Of all the modules, this is the highest priority for our lab's pipeline. Currently the N3 inhomogeneity correction module only accepts one volume, and the code doesn't appear to be open sourced (I don't see it off the CVS) so I can't take a stab at it. I think all it needs is a for-each loop around the algorithm (process each volume independently). Also, it seems the default setting for maximum number of iterations (50) is too low as this setting frequently leaves images with visible inhomogeneity remaining. Talking with Navid, he suggests 300 is preferred and I think it makes sense to make this the default for people less familiar with how all the various settings impact results.

Okay, thanks to the commented code from the Demons module I was able to write a wrapper for the IHN3 mipav dialog plugin that support volume collections. I found it very easy to match up the parameter names by recording the plugin as a script and then reading the script file.

If developers are allowed to edit the wiki I might add a section on building wrapper modules based on what I've learned.

Thanks guys, I'll give this a shot and report back.

Unless you are intimately familiar with the variables involved in the algorithm I would suggest using the commented code. This way if you do not change a variable, the default is used. Let me know if you have any questions about the code.

N3 is a MIPAV internal command that we have detected via the interface API, so the source is private the MIPAV. You can easily wrap these modules with JIST.

For an example of how to make a for-each wrapper, see the code by Blake Dewey. I prefer the section of code that he commented out, but either way would work.

package edu.vanderbilt.VUIIS.plugins;
public class DemonsRegCEST extends ProcessingAlgorithm