# CSCI 1951T Project 2 Handout

## What To Do Before Class

### Install Software on Paperspace Machines

On your Paperspace machines, install [Paraview 5.10.1](https://www.paraview.org/download/). To open Paraview, you will need to go to 'Program File' -> 'Paraview 5.10.1...' -> 'bin' in File Explorer, and 'paraview.exe' will be what you click to open the application.



Once Paraview has installed, go to 'Manage Plugins' under Tools, and ensure to have the OpenVR and the AnalyzeNIfTIReaderWriter plugins loaded by selecting them and clicking 'Load Selected'. **Unless you click autoload, you will have to load the plugins each time you open Paraview.**

The OpenVR plugin should be in the list. If the other one is not, you can download [AnalyzeNiftiReaderWriter](https://gitlab.kitware.com/paraview/paraview/tree/ec1fcdbbdd789a82591dd9c73e8408b029730d2a/Plugins/AnalyzeNIfTIReaderWriter), select 'Load New', select the file you downloaded, and it should appear.



In addition, via Steam, install [MEDICALHOLODECK](https://www.medicalholodeck.com/en/download-medical-metaverse/).

To run MEDICALHOLODECK, enter Virtual Desktop via your VR headset to connect to the Paperspace machine and then open the app. Once you open the app in VR, you will be asked to either enter your activation code for your license or start a free trial. **Click Start a Free Trial**.

You can find MEDICALHOLODECK tutorials [here](https://www.medicalholodeck.com/en/support/tutorials-manuals/medical-imaging-xr-virtual-reality-tutorials/#userinterface). **Please watch the tutorial for the controller interactions before class**.

## In-Class Activity

For Paperview, everyone will be working in pairs as the objective of this in-class activity is to compare collaboration between medical imaging softwares.

| Pair 1 | Pair 2 |Pair 3 |Pair 4 |Pair 5|Pair 6|
| --------| -------|-------|---------|------|------|
| Austin | Melvin |Camilo |Ashley |Yifei |Yuanbo|
| Brian | Vincent|Lexi |Mohammed |Dave |David |
| | | | | |Jakobi|

For MEDICALHOLODECK, you will be in groups of 4/5!

| Group 1 | Group 2 | Group 4 |
| ------ | ------- | -------- |
| Austin | Melvin | Ashley |
| Brian | Vincent | Mohammed |
| Yifei | Camilo | Yuanbo |
| Dave | Lexi | Jakobi |
| | | David |

### Paraview (10 Min)

Download this [Nifti file](https://drive.google.com/file/d/1QiWVdjMh_uIWPacQ8Jnfu9e9x2X-nqc6/view?usp=sharing).

On your Paperspace machine, open the downloaded file in Paraview. **The AnalyzeNiftiReaderWriter plugin needs to be loaded in order to view this file.**

You will see the file load in the Pipeline Browser. Click the closed eye to the left of the file name. Then, change the representation from 'Outline' to 'Volume'. If you are asked if you are sure you want to change, just click 'Yes'.


Now, your screen should look something like this:

#### VR Controls

In Paraview's OpenVR, only the right controller is used. You can use the **B button** to view the menu, and the right trigger is the only one you use to play with the data. On the bottom left of the menu, you can change what the right trigger does.


#### **Collaboration**

On your headset, enter Virtual Desktop so that you can see the Paraview app.

**Do the following steps ONE partner at a time**

Underneath OpenVR, click 'Send to Open VR'. If you cannot see the OpenVR window, go to 'View' and check 'OpenVR'.


Underneath Collaboration, change your name to what you would like your partner to see in the server, and then click 'Connect'. Now, your partner can do the same.

#### **To Dos**

1. Take a screenshot with your partner and the data in view.
2. Play with the data and the tools in the Paraview menu, and try to see something new with your partner. Then, fill out the Paraview section of this **[form](https://forms.gle/6u9PMLebpCpfEeVb8)**.

**N.B.** *Do not be alarmed by how uneventful Paraview is, there is truly not that much to do in VR directly. For example, it is not possible to change the display of the data through VR; you have to go through the computer.*

### MEDICALHOLODECK (10 Min)

Download this [DICOM file](https://drive.google.com/file/d/1KX_u9y6blKQs3S-p7i_zYXICyQoLT1_9/view?usp=sharing).

With your headset on Virtual Desktop, open MEDICALHOLODECK. On the left of the first screen you should see, under 'Medical Imaging XR', click the plus sign. This will open your local disk. If you saved your files to Downloads, just click downloads, click the file, and click 'Select'. (It will look like you didn't select the file, but you did!) The next screen will ask what data you wish to import: click '256 Slices' and 'Import 1 Dataset'.

  

#### VR Controls

You can find the VR controls video tutorial [here](https://www.medicalholodeck.com/en/support/tutorials-manuals/medical-imaging-xr-virtual-reality-tutorials/#userinterface).


#### Collaboration

One person in your group of 4 should be chosen to create the TeamXR room. Picture of instructions can be found below. **Load in the data after everyone has joined the room.**


#### **To Dos**

1. Take a screenshot with your group and the data in view. (I If not possible to get group into view, aim to get their hands in view?)
2. Play with the data and the tools in the MEDICALHOLODEC menu, and try to see something new with your group. Then, fill out the MEDICALHOLODECK section of the same **[form](https://forms.gle/6u9PMLebpCpfEeVb8)** as before.

### Finish The Third Section of the Form (5 Min)