baremetal.md

AutoCT

Installing Development Mode

Required Software

- Python (3.7)
- ANTs (2.3.1)
- FSL (5.0.10)

AutoCT Repository:

Clone the AutoCT repository.

git clone https://github.com/zhbai/AutoCT.git
cd AutoCT

Installation Using Conda:

conda create -n my-autoct python=3.7
conda activate my-autoct
python -m pip install .
# For devolopment mode 
python -m pip install -e .

Run Tools

## Workflow tools:
autoct-convert -h
autoct-preprocessing -h
autoct-bone-strip -h
autoct-registration -h
autoct-segmentation -h
autoct-label-geometry-measures -h 
autoct-warp-intensity-stats -h

## Template tools:
autoct-template-command-syn-average -h 

Example Workflow using illustration data.

The following commands allow you to run all the workflow steps.

## Inside container:
mkdir output
autoct-convert --use-dcm2niix 'notebooks/illustration_data/dcmfiles/*' output

autoct-preprocessing -m notebooks/illustration_data/MNI152_T1_1mm_brain.nii.gz 'output/*/convert/*.nii.gz' output

autoct-bone-strip 'output/*/preprocessing/*.nii.gz' output

autoct-registration -t notebooks/illustration_data/T_template0.nii.gz 'output/*/bone_strip/*.nii.gz' output

autoct-segmentation -a notebooks/illustration_data/New_atlas_cort_asym_sub.nii.gz 'output/*/registration/*/*.nii.gz' output

autoct-label-geometry-measures 'output/*/segmentation/*/*.nii.gz' output

autoct-warp-intensity-stats -a notebooks/illustration_data/New_atlas_cort_asym_sub.nii.gz \
   'output/*/registration/*/*.nii.gz'output

Running Example Jupyter Notebook

cd notebooks
jupyter nbextension enable --py widgetsnbextension
jupyter notebook notebooks/

Running Tests:

python -m pip install -e .
pytest tests