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docker instructions
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Christopher Reeder committed Jul 16, 2023
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Expand Up @@ -18,10 +18,29 @@ specialized encoders:
Multi-instance attention heads were then trained to integrate up to 40 view encodings to predict
a single measurement of each type per echo study.

## Requirements
In addition to the `ml4h` repository, DROID also requires `ml4ht_data_source` plus other dependencies. First, clone the
ml4h repositories:
```commandline
git clone https://github.com/broadinstitute/ml4h.git
git clone https://github.com/broadinstitute/ml4ht_data_source.git
```

For convenience, we provide a docker image containing additional dependencies:
```commandline
docker run -it --gpus all --rm -v {PARENT_DIRECTORY_OF_REPOS} -v {OPTIONAL_DATA_DIRECTORY} \
us-central1-docker.pkg.dev/broad-ml4cvd/droid/droid:0.1 /bin/bash
```

Within the docker container, install `ml4ht`:
```commandline
pip install --user ml4ht_data_source
```

## Usage
### Preprocessing
The following scripts are designed to handle echo movies that have been processed and stored in Lightning Memory-
Mapped Database (lmdb) files. We create one lmdb per echo study in which the keys are the filenames of the dicoms and
The following scripts are designed to handle echo movies that have been processed and stored in Lightning
Memory-Mapped Database (lmdb) files. We create one lmdb per echo study in which the keys are the filenames of the dicoms and
the values are echo movies that have been anonymized, cropped, and converted to avis. See `echo_to_lmdb.py` for an
example.

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