Template.config

# The configuration file consists of sections, led by a [section] header and followed by name: value entries,
# with continuations in the style of RFC 822 (see section 3.1.1, ?~@~\LONG HEADER FIELDS");
#
# time python baw_exp.py -processingLevel 2 -ExperimentConfig Template.config -pe IPL_ENVIRONMENT
#
# The intent of this configuraiton file is to define all the information needed to completely run an experiment.
#
[EXPERIMENT_DATA]
#   A formatted csv file decribing the data sets one per line
#  'PROJECT,SUBJ,SESSION,"[T1_1.nii.gz,T1_2.nii.gz]","[T2_1.nii.gz]"'
SESSION_DB=subject_db.csv
# The desired output directory for this experiment
EXPERIMENTNAME=B4AUTO.test

[IPL_ENVIRONMENT]
# Where to find BRAINSTools
BRAINSTOOLS_PATH=/Users/johnsonhj/src/BSA-Darwin-clang
# Where SimpleITK, required nipype, and other non-standard python packages reside
PYTHON_AUX_PATHS=/Users/johnsonhj/local/python-site-packages:/Users/johnsonhj/local/python-site-packages/lib/python2.7/site-packages
# Paths that need to be configured to find tools needed to run this workflow
PROGRAM_PATHS=%(BRAINSTOOLS_PATH)s/lib:%(BRAINSTOOLS_PATH)s/bin
# The path to the reference atlas spact to be used in this analysis by all BRAINSTools
ATLASPATH=%(BRAINSTOOLS_PATH)s/ReferenceAtlas-build/Atlas/Atlas_20120104
# The path to the model files to be used by BCD.
BCDMODELPATH=%(BRAINSTOOLS_PATH)s/BRAINSTools-build/ExternalData/TestData
# The prefix to add to all image files in the $(SESSION_DB) to account
# for different file system mount points
MOUNTPREFIX=""
# The base directory where all experiments of this type go
BASEOUTPUTDIR=/scratch/BRAINSAutoWorkUpTest/