Inital version of BRAINS AutoWorkup built on Nipype.  Currently very rough, use at your own risk!

To use the code, build Slicer4 with BRAINSTools and ITKv4 on.

Then install the nipype version in the BRAINSia github account.

Add the SEM plugin directory (something like /Slicer-superbuild/Slicer-build/plugins) to your path.

Run generate_brains_classes.py giving it the SEM plugin directory and the path/file to the slicer executable.

source /scratch/PREDICT/B4Auto_20111220_RUNS/bin/activate
export PATH=/scratch/PREDICT/johnsonhj/src/BRAINSStandAlone-Linux64-gcc44/lib:$PATH
python generate_brains_classes.py -p /scratch/PREDICT/johnsonhj/src/BRAINSStandAlone-Linux64-gcc44/lib

Add whatever directory you ran generate_brains_classes.py from to your python path.

You should now be able to run baw200.py.