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## Name
Visualise HNC Segmentation
## Description
This example creates a Hero Imaging workflow that visualizes the following:
1. CT and PET scan images of a patient's head and neck region.
2. Head and neck cancer (HNC) gross tumor volume (GTV) segmentations derived from manual annotation by an expert, a semi-automated algorithm (ATLAAS), and a deep-learning-based algorithm.
This workflow is created using the following Imaging nodes:
| Node name | Workflow Purpose|
| ------ | ------ |
| Import NIfTI | loads patient's CT image, PT image and HNC GTV segmentation masks from the respective NIfTI files. |
| Threshold | Converts GTV segmentations form Image to binary masks format. |
| Mask Contour | Produces the contour of the GTV in the binary mask image. |
| Visualize | Sends the images and masks to Hero Imaging Visualizer for Display |
## Visuals
![Simple Radiomics Workflow](https://git.cardiff.ac.uk./OyiboP/hero-imaging-workflows/-/raw/main/example_workflows/visualise_hnc_segmentation/visualise_hnc_segmentation.png?ref_type=heads)
## Getting Started
The following instructions will get Simple Radiomics workflow up and running on your Windows machine.
1. Start Hero Imaging. From the windows desktop or start menu
2. Open Existing Hero Imaging Workflow. From the **File** menu, select *Open*. Browse and select the *visualise_hnc_segmentation.ice* file in the **Open** window, click **Open**.
3. Add Existing Hero Imaging Database. From the **Database** panel click to *add an existing database file* button. Browse and select your *IBSI.sqlite* file in the **Open** window, Click **Open**.
3. In the **Settings** panel of the respective *Import NIfTI* node, change **Path** parameter value to the file path of the corresponding *NIfTI file* file. Browse and select your *.nii.gz* file in the **Select file** window, Click **Open**.
4. click *Start* button to run the workflow
5. click the *Visualizer* panel to view the output.
## Required Files
- [CT Image](https://git.cardiff.ac.uk./OyiboP/hero-imaging-workflows/-/blob/main/example_workflows/visualise_hnc_segmentation/CT_image.nii.gz)
- [PT Image](https://git.cardiff.ac.uk./OyiboP/hero-imaging-workflows/-/blob/main/example_workflows/visualise_hnc_segmentation/PT_image.nii.gz)
- [GT Mask](https://git.cardiff.ac.uk./OyiboP/hero-imaging-workflows/-/blob/main/example_workflows/visualise_hnc_segmentation/GT_mask.nii.gz)
- [ATLAAS Mask](https://git.cardiff.ac.uk./OyiboP/hero-imaging-workflows/-/blob/main/example_workflows/visualise_hnc_segmentation/ATLAAS_mask.nii.gz)
- [DL Mask](https://git.cardiff.ac.uk./OyiboP/hero-imaging-workflows/-/blob/main/example_workflows/visualise_hnc_segmentation/DL_mask.nii.gz)
- [HNC segmentation visualisation Workflow file](https://git.cardiff.ac.uk./OyiboP/hero-imaging-workflows/-/blob/main/example_workflows/visualise_hnc_segmentation/visualise_hnc_segmentation.ice?ref_type=heads)