Posted By: Stephen Damon - Dec 16, 2014
Tool/Resource: JIST: Java Image Science Toolkit
Merry JISTmas fellow JISTers!

Please see the minor release (JIST 3.2)

Since our previous release, we have fixed the following bugs:

1. The “Submit a Bug” now works correctly with all special characters.

2. XML returned by using the CLI interface now includes input/output for the directory channel which should help expedite integration with NiPy (thanks Chris!)

3. CLI STDOUT and STDERR are fixed to more logically represent what “went wrong” when you tried to run your module. Many times if a compulsory input was not passed to the CLI a generic error message about the module failing in an ungraceful manor would be returned. This generally reflects a developer error. However, in this case, this is not a developer error, but a parser error. Now it will return the required argument that you did not input.

4. Fixed many modules that would not run from CLI due to various parse errors which were all linked to having a special character for the argument.

5. Fixed a minor bug related to CLI which caused numerous modules to fail even though the args were correct. This was related to how the authors list was parsed.

New Features:

1. New Module under the MASI/External/Solar directory to run a polygenic model using SOLAR-ECLIPSE imaging genetics software: Note that the solar executable will need to be in your path.

2. We have expanded on our previous methods to implement various external CLI programs in the JIST environment. Utilizing a simple JSON framework, you are able to auto-generate modules for external CLI programs. Please see the wiki here: for a quick overview:

3. XML returned by the CLI is automatically tested to ensure that it is well-formed. If it is not, the first line of the output will be an error message. The Slicer XML will still follow.

Our next plans are to implement multi-shot DTI reconstruction and ASL processing modules.

Best wishes and have a safe and happy holiday,
Benentt and Steve @ Vanderbilt
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