Image segmentation (MABS) commands

MABS can be run in several modes. These modes are described here.

Command	Description
convert	Convert an atlas data set from DICOM-RT into nrrd for use by MABS.
pre-align	Does this work?
train-registration	Add description here.
train-atlas-selection	Add description here.
train	Add description here.
atlas-selection	Add description here.
segment	Use MABS to segment the specified image.

Convert

Convert a set of atlases. The input images are found in the directory specified by the “atlas_dir” field in the [TRAINING] section. The output are placed in the directory specified by the “convert_dir” field of the [TRAINING] section.

If images are already converted into nrrd format, this command may be omitted.

Pre-align

To run the pre-alignment command, you must set the “mode” field in the [PREALIGN] section to “custom”.

The pre-align command takes images from the directory specified by the “convert_dir” filed of the [TRAINING] section as input. The output images are placed into the dirctory specified by the “training_dir” field of the [TRAINING] section.

Note, pre-alignment is also used in atlas selection. No documentation on this yet.