Each module of PNEURO 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
Note that there are differences in the execution of protocols. When loading a Maximum Probability 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, including the MR segmentation. The Apply PET to Anatomical transformation allows using a saved transformation instead of performing the actual matching calculations. Either the transformation saved with the protocol can be used (default), or an external transformation file can be loaded. If the Use VOIs contained in protocol (skip segmentation) option is enabled, the outlining is not performed, but rather the saved VOIs are retrieved. This has the advantage that any manually adjusted VOIs are recovered. Please note that manual adjustment of the transformation is not possible when VOIs from the protocol are used. With Calculate Statistics the VOIs will be applied to the data at the end of the protocol.
When loading a Brain Parcellation protocol, the same options are shown. However, note that when the Use VOIs contained in protocol option is enabled neither the segmentation nor the parcellation is performed. Consequently, a parcellation protocol will be executed faster than a Maximum Probability protocol.
VOIs and Protocol Execution
In case of the step by step interactive procedure the regions for which the atlas description is set to H will NOT be selected on the Group tab. The VOIs definitions and settings on the Group tab will be store into the protocol.
•If Execute after loading is enabled but the Calculate Statistics box disabled the processing ends up on the VOIs page with the settings available at the moment of protocol saving. The VOIs outlining is performed as part of the protocol processing.
•If Execute after loading and Calculate Statistics boxes are enabled the statistics results will be returned for all VOIs, independently of the settings on the Group tab at the moment of the protocol saving. The VOIs outlining is performed as part of the protocol processing. This behavior was enforced for the batch processing to return the results for all the corrected regions.
•If Execute after loading and the Use VOIs contained in protocol (skip segmentation) option is enabled the saved VOIs from the protocol are retrieved. Outlining of the VOIs is not performed anymore. This has the advantage that any manually adjusted VOIs are recovered, while restoring the selection settings on the Group tab at the moment of protocol saving.