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 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 Use protocol units sets image data units to the units of protocol original images. 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 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 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.