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update README
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gamorosino committed Dec 23, 2021
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Expand Up @@ -138,3 +138,13 @@ run_test_local.sh <download_dir.ext> <output_dir>
```
The script performs the automatic download of the published testset (using [`brainlife CLI`](https://brainlife.io/docs/cli/install/)) of the DBB benchmark (https://doi.org/10.25663/brainlife.pub.24) in the folder ```<download_dir>```. Then, the script predicts the segmentation volume for each subject and stores the results in ```<output_dir>```.
Finally, compute the dice score using the published ground-truth and create the final _csv_ file, _average_dice_score.csv_ (stored in ```<output_dir>```), reporting the average dice score across the subjects for each label of the segmented volumes.

If you use this code for you research please cite:

```
Amorosino G. et al. (2020) Automatic Tissue Segmentation with Deep Learning in Patients with Congenital or Acquired Distortion of Brain Anatomy. In:
Kia S.M. et al. (eds) Machine Learning in Clinical Neuroimaging and Radiogenomics in Neuro-oncology. MLCN 2020, RNO-AI 2020. Lecture Notes in Computer
Science, vol 12449. Springer, Cham. https://doi.org/10.1007/978-3-030-66843-3_2
```

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