requirements.yaml

channels:
  - defaults
  - conda-forge
  - anaconda
  - bioconda
dependencies:
  - python=3.8
  - numpy
  - nibabel
  - itk
  - simpleitk=2.0 # get rid of ITK ERROR: ITK only supports orthonormal direction cosines.  No orthonormal definition found!
  - scikit-image
  - pillow
  - pandas
  - matplotlib
  - tqdm
  - omegaconf
  - gdown
  - synapseclient # command-line tool to download from synapse.org
  - monai # this repo uses monai.app.utils to extract zip files. is it too much? because of this dependency, we have to pull other repos such as pytorch which are not needed here