# Imaging setup

## Requirements

1. **3D Slicer:** [3D Slicer](https://download.slicer.org/) (v >= 5.2.2) together with the SlicerNetstim, SlicerOpenIGTLink and SlicerIGT extensions should be installed.
2. **ORScene:** An *ORScene* is a file that includes subject images, planning information and atlas-based segmentations ready to loaded into Slicer. It can be created from Lead-DBS and an example dataset is already included in the SlicerNetstim extension.

## Loading sample ORScene

A sample ORScene is included to test the platform. To load it follow the next steps:

1. Open Slicer.
2. Switch to Sample Data module.
3. Scroll down and select STN Planning.

See the following screenshots as reference:

<figure><img src="https://652347722-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FaEKrtfptpsNlKGfPk7Bs%2Fuploads%2FWjiUFsweVFAgymlxRhjI%2FswitchToSampleData.png?alt=media&#x26;token=7ba163d3-2520-40dc-bab4-9c267c65ae15" alt=""><figcaption><p>Step 2: Switch to Sample Data module.</p></figcaption></figure>

<figure><img src="https://652347722-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FaEKrtfptpsNlKGfPk7Bs%2Fuploads%2Fv4w9p3vrv9v9DyrOsPlZ%2FselectSampleData.png?alt=media&#x26;token=50bc893a-afa4-436c-9f0e-ff747418d684" alt=""><figcaption><p>Step 3: Select STN Planning ORScene.</p></figcaption></figure>

## Creating new ORScene

In order to create an ORScene follow the next steps:

1. Process a subject in Lead-DBS with the **co-registration** and **normalization** steps.
2. Place the surgical planning files under a `leador` subfolder within the subject folder.
3. Load the subject in Lead-DBS and select `Tools > Lead-OR > Create ORScene`. Note that the selected atlas will be put into the scene as well.
4. Drag and drop the `ORScene.mrb` file into Slicer.

See the following screenshots as reference.

<figure><img src="https://652347722-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FaEKrtfptpsNlKGfPk7Bs%2Fuploads%2FQZRFh6SIROAgDBBUiXUk%2FScreenshot%202023-03-16%20at%2018.02.11.png?alt=media&#x26;token=e14fc836-4068-4310-add2-4ae5e933cfe3" alt=""><figcaption><p>Step 2: Lead-DBS subject processed and with Brainlab planning files in respective folder.</p></figcaption></figure>

<figure><img src="https://652347722-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FaEKrtfptpsNlKGfPk7Bs%2Fuploads%2FUrZdX8DtjyNSQFesTWI5%2FScreenshot%202023-03-16%20at%2017.30.22.png?alt=media&#x26;token=a3b24fce-49f8-4956-b399-5f35d950c80e" alt=""><figcaption><p>Step 3: Create ORScene from Lead-DBS.</p></figcaption></figure>

<figure><img src="https://652347722-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FaEKrtfptpsNlKGfPk7Bs%2Fuploads%2FTjZvFQ8Kr7VKJ4Pz4ufl%2FScreenshot%202023-03-16%20at%2018.01.51.png?alt=media&#x26;token=4fae4e5f-38f8-49e7-9f04-b1d8b4db7466" alt=""><figcaption><p>Step 4: Output folder with file to load into Slicer.</p></figcaption></figure>