PNROD allows saving the final processing configuration as a protocol.
Such a protocol includes definition of the input data as well as the parameters of the different processing stages, including parametric mapping. The user is advised to save a protocol after every completed data processing workflow, so that at any later time the configuration can be retrieved, verified and modified to try variations of the processing parameters.
Note: If parametric mapping should be part of the protocol, page Parametric Mapping must be active when saving the protocol.
Protocol Execution
When loading a PNROD protocol a dialog window offers several options.
If Execute after loading is enabled, not only the configuration is retrieved, but the processing is also performed with the following options:
•The Apply INPUT to Anatomical transformation allows using a transformation instead of repeating the actual rigid matching in a dual-modality workflow. Either the transformation saved with the protocol can be used (default), or an external transformation file can be specified.
•If the Use VOIs contained in protocol option is enabled, region outlining is not executed, but rather the saved VOIs are retrieved. This has the advantage that any manually adjusted VOIs are recovered.
•With Calculate Statistics the statistics in the VOIs will be calculated at the end of the protocol.
Please note that if information is retrieved from the protocol instead of repeating all processing, not all processing options will be active.
Note that protocols may also be executed from the command line using a modified PMOD start script:
The tool must be defined immediately following "pmod.jar", separated by a space, then the paths to the protocol and input data defined, also separated by spaces.