This code provides a simple framework for building pipelines for medical image processing tasks.
Using the basic pipeline-building code requires python with numpy.
Using the image registration tools currently available requires the ANTS image registration toolkit.
Using MATLAB-compiled commands (MCC) requires the MATLAB Compiler Runtime (MCR).
For an example, see regpipe.py, which implements the registration
pipeline described in the paper:
Quantification and Analysis of Large Multimodal Clinical Image Studies: Application to Stroke by Sridharan et al.
To construct your own pipeline, you can use this script as a baseline
or build your own. Create Command objects from pipebuild.py in the
order you want them executed, just like you would with a shell script.
At the end, use Command.generate_code() to write a shell script to
a file. You can run this file either from within python using subprocess,
using a cluster with SGE as in regpipe.py, or using any other method
you prefer.
File structure is dictated by the Dataset class in pipebuild.py. The code is
currently built around the assumption that there's a single atlas image, but
this will be generalized in a future update. Files are organized according to
the templates in the get_file() method of Dataset. The organization of your
original images (before being input to the pipeline) can be specified in the
get_original_file() method of Dataset.