We currently have a number of initial models at MICe that are setup for use with Pydpiper.
They can be found in:
Some common initial models are:
The proper command line options for each are:
(40 microns) --init-model=/hpf/largeprojects/MICe/tools/initial-models/Pydpiper-40-micron-basket-dec-2014/basket_mouse_brain_40micron.mnc
(56 microns) --init-model=/hpf/largeprojects/MICe/tools/initial-models/Pydpiper-56-micron-basket-may-2014/basket_mouse_brain.mnc
(90 microns) --init-model=/hpf/largeprojects/MICe/tools/initial-models/Pydpiper-MEMRI-90micron-saddle-july-2015/p65_MEMRI_mouse_brain.mnc
For the first part of the registration process, a registration target is required. One may be provided in the form of an initial model, or the code can "bootstrap" (use one of the input images as a target).
Two options are available when specifying an initial model:
Whether you are using options 1 or 2 above, the command line option specified is the same:
Note that for this example, we have used the name image.mnc, but you can use any name you'd like, provided you follow the naming conventions described below. In all cases, the given file contains an image in standard space.
Whether you execute options 1, 2, or 3 depends on the other files contained in the same directory as image.mnc. Based on the files contained there, the code will know which option to use:
The specified naming conventions MUST be followed, or the code will not work.
To make initial models for option 2, consider this page: Creating an Initial Model.