<commit_before>#!/usr/bin/env sh 

# please make sure you installed all dependencies of NiftyNet.
# cd NiftyNet/; pip install -r requirements-gpu.txt
NIFTYNET=../../run_application.py

DIR="$( cd "$(dirname "$0")" ; pwd -P )"
cd "$DIR"

# download OASIS dataset ~7MB
sh ../../data/brain_parcellation/get_oasis_data.sh

# download a trained HighRes3DNet parameters
sh get_highres3dnet_model.sh

# run brain parcellation
python -u $NIFTYNET inference -c ./highres3dnet_config_eval.txt --image_size 160 --label_size 160
<commit_msg>Issue #69: revised demos/brain_parcellation/run_parcellation.sh for the imminent removal of run_application.py<commit_after>#!/usr/bin/env sh 

# please make sure you installed all dependencies of NiftyNet.
# cd NiftyNet/; pip install -r requirements-gpu.txt
NIFTYNET=../../niftynet/__init__.py

DIR="$( cd "$(dirname "$0")" ; pwd -P )"
cd "$DIR"

# download OASIS dataset ~7MB
sh ../../data/brain_parcellation/get_oasis_data.sh

# download a trained HighRes3DNet parameters
sh get_highres3dnet_model.sh

# run brain parcellation
python -u $NIFTYNET inference -c ./highres3dnet_config_eval.txt --image_size 160 --label_size 160

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{'dir': 'git-commits-cleaned', 'id': '3423885', 'n_tokens_mistral': 433, 'n_tokens_neox': 398, 'n_words': 113}