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update readme #220

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Apr 8, 2024
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update readme #220

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15 changes: 13 additions & 2 deletions README.md
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Expand Up @@ -24,7 +24,7 @@ This repository contains 3 major modules:


## **Current Version**
VesselBoost 0.9.1
VesselBoost 0.9.4

## **Requirements**
- Docker / Singularity container
Expand All @@ -38,9 +38,20 @@ VesselBoost, pre-trained models, and required software are packaged in software
The Dockerhub container is available at Dockerhub. To download the container, run the following command:

```
docker pull vnmd/vesselboost_0.9.1
docker pull vnmd/vesselboost_0.9.4
```

### Neurodesk
To predict vessel segmentation using your data and the latest version of VesselBoost on Neurodesk, you can run the following code snippet:

```bash
ml vesselboost
path_to_model=/cvmfs/neurodesk.ardc.edu.au/containers/vesselboost_0.9.4_20240404/vesselboost_0.9.4_20240404.simg/opt/VesselBoost/saved_models
prediction.py --ds_path /path/ --out_path /path/ --pretrained "$path_to_model"/manual_ep1000_1029 --prep_mode 4
```

For more information, please check our [notebooks](https://github.com/KMarshallX/VesselBoost/tree/master/notebooks).

## **Installation**
This is a Python-based software package. To successfully run this project on your local machine, please follow the following steps to set up the necessary software environment.

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