DeepLungScreening/example.txt at main · MASILab/DeepLungScreening · GitHub

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Please download the docker image use:

docker push rg15/deeplung:0.3

after download docker image:

rg15/deeplung:0.3

One example to run is:

sudo docker run -u root -v /your/local/INPUTS:/INPUTS/ -v /your/local/OUTPUTS:/OUTPUTS deeplung:0.3 sh run_all.sh

I will share a INPUTS example that can run via vanderbilt box shortly.

The path:

the local input path:

/your/local/INPUTS

The local output path:

/your/local/OUTPUTS

You can change the local input / output paths as you want.

In my local input path:

a csv file: "test.csv" includes the scans you want test and the meta data information.

a fold: "NIfTI" stores the image you want to process.

The output path will generate:

a fold: "prep" stores the preprocessed image from the original nifti.

a fold: "bbox" stores the detected lung nodule location.

a fold: "feat" stores the image feature extreated from nifti.

a csv file "pred.csv" stores the predicted cancer probability (not calibrated).