Below is a list of options included for all registration pipelines.
--pipeline-name: This is analogous to the option of the same name in the old version of MICe-build-model. It is the prefix for the _nlin, _lsq12, _lsq6 and _processed directories that we often use in iterative model building.
--mask-dir: If you'd like to specify a mask for each of your input files, you may place it into a directory, and specify this directory when running your pipeline. Two options are available:
- A single mask may be specified for all input brains. If this is desired, only one mask should be placed in the specified directory.
- A unique mask may be specified for each input. If this is desired, the same number of masks as inputs must be placed in the directory, and named appropriately. (e.g. imageA.mnc would correspond to imageA_mask.mnc and so forth.) If this naming convention is not used, the program will exit with an error.
- NOTE: If this directory is not specified, no masks will be associated with the specified input files.
--registration-method (i.e. the ability to specify minctracc or mincANTS as a non-linear registration method) is currently included as a general registration option, but will be removed shortly. The ability to specify one or the other will become more specific to each registration module. For now, specify minctracc (default) or mincANTS as desired, with the knowledge that it will apply to all non-linear alignments performed for a specific registration call.