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gamorosino committed Oct 6, 2022
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Expand Up @@ -77,6 +77,8 @@ To avoid using the config file, you can input directly the fullpath of the files
main.sh <t1.ext> <mask.ext> [<outputdir>]
```

If you want to avoid performing the histogram matching on the reference image, you can specify the ```--no-histmatch``` option

#### Script Dependecies

The App needs `singularity` to run.
Expand Down Expand Up @@ -149,4 +151,4 @@ or with local softwares installed:
run_test_local.sh <download_dir> <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, the script computes the dice score between the predicted segmentation and the test set ground-truth, and create the final _csv_ file, named _average_dice_score.csv_ (stored in ```<output_dir>```), reporting the average dice score across the subjects for each label of the segmented volumes.
Finally, the script computes the dice score between the predicted segmentation and the test set ground-truth, and create the final _csv_ file, named _average_dice_score.csv_ (stored in ```<output_dir>```), reporting the average dice score across the subjects for each label of the segmented volumes.

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