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You can download the Singularity container here: link.

While you can find the docker here: link.

Testing tutorial

Steps for singularity (similar to docker):

1. Download the container and the code from Github

   wget https://osf.io/download/v8g9x/ && mv index.html LOD_Brain.simg

   git clone https://github.com/rockNroll87q/LOD-Brain

2. Prepare your testing data. As an example, I download a volume from a public repository (link):

   wget https://s3.amazonaws.com/openneuro.org/ds002207/sub-01/anat/sub-01_T1w.nii.gz

   wget https://s3.amazonaws.com/openneuro.org/ds002207/sub-02/anat/sub-02_T1w.nii.gz

3. Run the container:

    singularity exec --cleanenv --nv \
    -B {PATH_TO_YOUR_TESTING_DATA}:/data/ \
    -B ./LOD-Brain/src:/source/ \
    -B ./LOD-Brain/trained_model/:/model/ \
    -B {WHERE_YOU_WANT_TO_SAVE_THE_OUTPUT}:/output/ \
    LOD_Brain.simg python /source/inference.py --vol_in=/data/
   

   Example:

    singularity exec --cleanenv --nv \
    -B ./:/data/ \
    -B ./LOD-Brain/src:/source/ \
    -B ./LOD-Brain/trained_model/:/model/ \
    -B ./:/output/ \
    LOD_Brain.simg python /source/inference.py --vol_in=/data/
   

   In vol_in you can pass a folder, for example vol_in=/data/, or a volume like vol_in=/data/sub-01_T1w.nii.gz

FAQ

A. If you get the error ModuleNotFoundError: No module named 'tensorflow_addons'

$ singularity shell --cleanenv --nv LOD_Brain.simg
$ python -m pip install tensorflow-addons