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======Simulation Assisted Navigation for Skull Base Surgery======
**Last updated: Date and time**


======Summary======
Skull base surgery usually has delicate and complex surgical procedures, so surgeons hope to know the detailed real-time information of the operation so that the critical regions won’t be hurt and damaged.For example, surgical drills intend to remove the bony tissue rather than soft tissue. If the soft tissue is beneath the bony tissue, surgeons need to know how far soft tissue is located from the current position.

The project goal of our project is to provide immersive, detailed, and real-time navigation for surgeons. Our task is to develop a pipeline for augmenting stereo mircoscopic video with AMBF simulation for guidance in skull base surgery. While doing the surgery, the surgeons should be able to pause the operation and load the simulated anatomy onto the main view to get an idea of how far they have drilled and what anatomies are nearby. They are also able to change the view of the simulated anatomy like, rotation, scaling, and slicing.

  * **Students:** Xinhao Chen, Zhaomeng Zhang
  * **Mentor(s):** Dr. Adnan Munawar, Dr. Manish Sahu, Max Li, Mohammad Salehizadeh, Dr. Peter Kazanzides, Dr. Pete Creighton, Dr. Danielle Trakimas, Dr. Deepa Galaiya, Dr. Russ Taylor

======Background, Specific Aims, and Significance======
The skull base surgery is a specialized operation closely related to neurosurgery and
otolaryngology, which surgeons need to access the skull of a patient to treat the diseases
[1]. Pituitary tumors, meningiomas, and chordomas are the diseases requiring skull base
surgery [4]. In certain types of skull base surgery, the bony tissue must be removed by
surgical tools in order to reach the target anatomy. However, it is a difficult and
complicated procedure for surgeons for two reasons.

Patients usually have different anatomy structures in some surgical regions. For example,
male patients usually have thicker and larger skull bones, but the skulls of females are
generally thinner and lighter [6]. And male eye sockets are squarer than females [6]. The
sex is only one factor that can make an individual's skull different from others. These
distinct skull structures increase the difficulty of doing the operation for surgeons.
Therefore, surgeons hope to have a stereo anatomy model of patients as reference during
the surgery, which is one motivation for our project.

Moreover, the real-time and detailed navigation information could greatly assist the skull
base surgery and lower the risk of operation [1]. During the operation, the surgical drills
intend to remove the bony tissue rather than soft tissue, and if the soft tissue is beneath
the bony tissue, surgeons are not able to see it, so they need to know how far soft tissue is
located from the current position of surgical drill in real-time for making sure sensitive
tissue won’t be hurt and damaged. To provide concrete and real-time operation
navigation information for surgeons is the second motivation for our project.

{{ :courses:456:2023:projects:456-2023-13:screenshot_2023-04-10_154817.png?600 |}}

Figure 1 The fully immersive virtual reality system [4]

A fully immersive virtual reality system (FIVRS) has been developed and designed for practice of skull base surgery. The system works on the fundament of Asynchronous Multi-Body Framework (AMBF) which is “an open-source 3D versatile simulator for robots and provides a real-time dynamic simulation of multi-bodies such as robots, free bodies, and multi-link puzzles.” [5] Based on AMBF, our mentors developed FIVRS in recent years. To run the FIVRS requires a lunch file that consists of a world file, input device file, and model file. These three files are three types of AMBF Description Format (ADF) Files [1]. According to Figure 1, the world file has env model file and world attributes that can be solver attributes, gravity, and dimensions. The env model file is formed by the model file which can be bodies, joints, sensors and actuators, and multiple model files can be loaded in the launch file [1]. The overall model loading flow for FIVRS is described in Figure 1. 

Compared with AMBF, the rendering pipeline and AMBF Description Format (ADF) specifications are improved for AMBF+ [1]. Additionally, the modular plugin handling interface in AMBF+ allows users to do custom application development [1]. 

{{:courses:456:2023:projects:456-2023-13:picture1-1.png?400|}}

Figure 2 The overall model loading flow for AMBF+ [1]

Fully immersive virtual reality system allows users to load stereo anatomy models from actual Computer Tomography (CT) of patients and accepts various input devices, including stereoscopic display (VR headset), haptics device, keyboard, 6D mouse, and foot pedal (Figure). With these input devices, surgeons can have an immersive stereoscopic view of anatomy and control the virtual drill to do the operation in the simulation environment. In the meanwhile, the system is able to generate valuable data for downstream algorithm development and surgical assessment of surgeons [1].
======Deliverables======
 
  * **Minimum:** (2023/3/25)
    - A environment that can run AMBF codes.
    - An AMBF plugin that can read the stereo video from stereo microscope.
    - An AMBF plugin that can process the stereo microscopic video for HMD.

  * **Expected:** (2023/5/10)
    - A system with small latency time.
    - A system can display both simulation and anatomy videos in HMD.
    - An user interface for switch and control two videos.
    - An updated system with registration.

  * **Maximum:** (Summer Holiday)
    - A system can be applied in real skull-base surgery.
    - Conduct user study with surgeons and write a user study report.
    - Present the system and findings in a paper.

======Technical Approach======
**1. Overview**

{{ :courses:456:2023:projects:456-2023-13:system_overview.png?600 |}}

Figure 3 Workflow of the system

Figure 3 shows the workflow of our system. It can be divided into two parts, the users’ part and the system part. As we mentioned in the motivation, skull base surgery is hard. The aim of our system is to assist surgeons by showing everything more clearly.

We have a stereo microscope to produce real time video from surgery. We also have CT scan before surgery to construct the model in AMBF+. We already have ICP (Iterative Closest Point) registration through optical tracker system between real time video and simulation environments to connect them together.[6] This step enables the drill in AMBF+ to move and cut the same thing as the drill in real surgery. Then, we process both videos and transmit them to HMD. Surgeons can see both real time video and simulation video in HMD. They have many choices for simulation videos. They can see the model from any point in any angle or see slices instead of 3D models.

Our task mainly focuses on the system part. We already have all the hardware and AMBF+ platform. The task we need to do is to connect all parts together and make them a whole system. We will start with the ROS (Robot Operating System) and CV_bridge  package to process videos. If we want to further decrease the latency time, we may explore additional protocols and software such as Gstreamer. CV_bridge  package fills the gap between getting raw images from a camera driver and higher-level vision processing by OpenCV. It can process raw camera images into useful inputs to vision algorithms. Since AMBF+ is also based on ROS in C++, they can cooperate well.

We will use HTC VIVE Pro HMD to display videos. Built to meet the needs of today’s most demanding VR users, VIVE Pro is an easy-to-deploy VR system that provides the richest feature set for professional users. From seated environments to expansive, multi-user deployments, VIVE Pro delivers the highest fidelity, clearest audio, and most immersive VR experience. 

**2. Reading videos**

The system we aim to develop needs two kinds of videos, one from AMBF simulation platform and the other one from real microscope. To make the system work, we should develop two methods to read a group of stereo videos from each source. A group of stereo videos contains a video for the left eye and a video for the right eye.

{{:courses:456:2023:projects:456-2023-13:picture1-2.png?400|}}

Figure 4 Hardware pipeline for reading videos

Figure 4 shows the hardware pipeline for reading videos. We first adjust stereo microscope to see models clearly. Then, the camera will record videos from microscope and transmit it to the lab computer. The lab computer is connected to a router, and we also connect our computer to the router through an internet cable. We do not use WIFI connection because the bandwidth may not be big enough for high resolution videos. Till now, videos from the real microscope are transmitted to our computer. 

Meanwhile, the AMBF simulation platform is running on our computer to generate another group of videos. We process both groups and finally display them on HMD.

{{:courses:456:2023:projects:456-2023-13:picture1-3.png?400|}}

Figure 5 Operating Haag-Streit microscope

Figure 5 shows the stereo microscope. The type of it is the Haag-Streit microscope. Haag-Streit delivers breakthrough versatility and precision in microscope technology for ophthalmology. With over 140 years of experience in surgical tool manufacturing, they set the standard for optics, ergonomics, engineering, and imaging. This surgical microscope provides best-in-class stability and 3D perception.

To use it, we first need to remove the protective cover on it. And then open the green switch on the side. There are many buttons on both sides’ handles, which can move the camera, adjust the light and focus. During the usage, we should take care not to touch the lens or they will be polluted and make the video vague. After using it, we need to close the switch and put the protective cover back. It is important to close the switch because the light of the microscope is strong and can produce huge heat after running for a long time.

{{:courses:456:2023:projects:456-2023-13:picture1-4.png?400|}}

Figure 6 Sony MCC-3000MT 3D Full HD Medical Video Camera

After adjusting the stereo microscope, we need to use a camera to record videos from it. The camera we use is “Sony MCC-3000MT 3D Full HD Medical Video Camera”, as shown in figure 6. Since everything is already set and connected, we just need to open the camera when using it and close it before we leave. One thing that needs to be noticed is the focal plane of the camera is determined by the microscope but not itself. The camera publishes videos as ROStopics.

The video recorded by Medical Video Camera is transmitted to the lab computer. Since a lot of research projects need that computer, it is not recommended to install packages and do video processes on that computer. A router is used to transmit videos from that computer to our own computer, as shown in figure 7.

{{:courses:456:2023:projects:456-2023-13:picture1-5.png?400|}}

Figure 7 Router

We need to connect both computers to the router through internet cables. A special type of internet cable is required to prove the speed of transmission.

It is easier to read videos from AMBF simulation platform than the ones from real microscope because the video is generated in the computer. AMBF simulation platform provides functions for setting camera at any position. We just need to set camera parameters in the file "./ADF/single_stereo_camera.yaml". The videos are published as ROStopics, which is the same as the real camera.

Since both groups of stereo videos are in ROStopics, we can subscribe to what we need to read them.

**3. Processing videos**

The videos we read from real microscope or AMBF simulation platform are designed to display on normal screens but not VR videos for HMD. If we directly display them in HMD, people cannot see anything clearly in it and will feel dizzy. That is why we need to process videos in proper type for displaying.

The method to process normal videos into VR type is giving distortion.[7] There are a total of 6 parameters that have to do with lens correction. First, there is the lens Field of View. It is a parameter that determines image perspective distortion. The actual lens correction parameters a, b and c, which are used to correct for barrel distortion, pincushion distortion and even wavy distortion, as shown in figure 8. The lens shift parameters d and e that correct for the lens optical axis not being in the image center.

{{:courses:456:2023:projects:456-2023-13:屏幕截图_2023-05-10_155844.jpg?400|}}
            (a)                          (b)
{{:courses:456:2023:projects:456-2023-13:屏幕截图_2023-05-10_160019.jpg?400|}}
            (c)                          (d)        
Figure 8 Distortion types [7] (a) Raw image (b) Barrel distortion (c) Pincushion distortion (d) Even wavy distortion

The Focal Length is a physical property of the lens. We can change it by operating the microscope. Together with the effective sensor or film size and the focusing distance it approximates the image Field of View. The Field of View together with the lens projection determines the image perspective distortion. 

The lens distortion a, b and c parameters correspond to a third-degree polynomial describing radial lens distortion.

{{:courses:456:2023:projects:456-2023-13:picture1-6.png?400|}}

This equation shows how it works. “rdest” and “rsrc” refer to the normalized radius of an image pixel. The center point of this radius is where the optical axis hits the image. Normalized means here that the largest circle that completely fits into an image is said to have radius equals 1. The fourth parameter d is determined by a, b, and c by d = 1 – a – b - c.

In our program, all parameters are set in file "./plugin/camera_hmd/hmd.cpp" and the distortion is written in file "./plugin/camera_hmd/shaders/hmd_distortion.fs". Detailed information of how we realize it in codes can be found in our documentation GitHub README.md [8].

**4. Displaying videos**

After processing both groups of stereo videos, we need to display them in head-mounted display (HMD). It is a display device, worn on the head or as part of a helmet, that has a small display optic in front of each eye.

{{:courses:456:2023:projects:456-2023-13:picture1-7.png?400|}}

Figure 10 VIVE Pro headset [9]

The HMD we use for this system is the VIVE Pro headset. It has next-level graphics and sound for riveting PC-VR. Its purposeful and pragmatic ergonomics delivers smooth and comfortable immersion.

When using it, we need to connect it to our computer through two cables, one USB and one USB-PD. The HMD also needs an individual power source. It works as a second screen for the computer. Detailed information of all hardware we used for this system can be found in our documentation Hardware Setup Manual [9].

To display processed video in the HMD, we should set it display in the second screen in full-screen mode. It can be set in file "./ADF/single_stereo_camera.yaml". There will be a normal video showing AMBF simulation platform in computer screen while VR views in HMD.

**5. Registration**

The registration method is mainly following Twin-S system.[6] It is based on optical tracker system.

{{:courses:456:2023:projects:456-2023-13:picture1-8.png?400|}}

Figure 12 Overview of Twin-S for skull-base surgery [6]

Building a digital twin system for skull-base surgery requires precise modeling, tracking, and updating of the patient’s anatomy, the surgeon’s tool(s), and the surgical camera. In the paper, the system includes a surgical phantom to simulate the patient’s anatomy, a surgical drill as the ablation tool, and a stereo surgical microscope.

For each object, there are 2 frames. They are the base coordinate and the local coordinate. The base frame is used to localize the position and orientation of the object while the local coordinate is related to the function of the object. Optical markers are fixed on the base frame.

The base frame of the surgical drill is at the tail of the drill shaft, together with the optical tracking markers. The drill local coordinate frame is on the drill tip center. For the rotation part of the transformation between these frames, there are only 2 degrees of freedom because the drill is symmetrical along its shaft. To find the shaft axis in optical tracker coordinate, they fix the drill on a robot arm end effector, where the drill holder aligns the drill shaft with the Z-axis of the robot to sufficient accuracy. Therefore, by commanding the robot to move along its Z-axis, we recover the direction of motion Q in the optical tracker coordinate.

They obtain the 3D structure of the surgical phantom using a CT scanner. The phantom is modeled as a binary volume of occupancy, where voxels corresponding to the bony tissues are marked as occupied and voxels representing air are marked as free space. To track the surgical phantom, they mount the phantom on a polycarbonate board with optical tracking markers, defining the base coordinate of the phantom. To calibrate the transformation from phantom base to phantom, they directly compute the transformation between the virtual model and the physical phantom via the point-to-plane ICP registration. They sample 380 points on the physical phantom surface using a tracked pointer tool for the purpose of calibration.

When surgeons perform drilling in the real world, the system updates the surgical phantom in real-time. They approximate the drill tip as a sphere. Twin-S detects collisions between the surgical phantom and the drill burr given the tracked positions. The voxels that collide with the drill tip sphere are moved and set to free space to simulate the tissue removal process.

The paper obtains the intrinsic parameters and distortion coefficients of the stereo camera using a ChArUco pattern. Rectification is then performed to obtain a projective camera model. To track the surgical camera, optical tracking markers are mounted on the handle of the camera, defining the base coordinate frame. A hand-eye calibration routine [10] is used to obtain the transformation. Given the tracked camera, Twin-S generates per-pixel segmentation masks and depth maps based on the object information, which can be used for different downstream applications.

With the help of mentors, we have already prepared everything for registration. However, due to the limited time, we have not integrated registration to our system. We plan to finish this in the summer holiday.

**6. User interface**

We designed four different modes for displaying videos, as shown in Figure 13. Actually, they are the combination of two groups of stereo videos.

We can only display one video on the whole screen of HMD. Or we can display two videos, one on the big screen while the other one on a small window on the side. Both videos can have 3D views in this mode.

To switch between these modes, we can develop a GUI based on AMBF’s GUI. Figure 14 shows the GUI of AMBF. We may replace the left part with four modes and keep other buttons the same. We may also set shortcuts on the keyboard to switch between these modes.


======Completed Work======
**1. The result of read mircoscopic video in AMBF plugin:**

{{ :courses:456:2023:projects:456-2023-13:screenshot_from_2023-04-08_11-00-20.png?600 |}}

**2. The result of processing mircoscopic video for HMD:**

{{ :courses:456:2023:projects:456-2023-13:screenshot_from_2023-04-10_09-44-01.png?600 |}}

**3. User interface viewing design:**

{{ :courses:456:2023:projects:456-2023-13:screenshot_2023-04-10_201544.png?600 |}}

**4. Minimize the latency time:**

We are using rostopic to transmit videos. The current latency time is about 0.3 second, which we think is good enough for now.
======Discussion======
During this semester, we successfully developed a pipeline for augmenting stereo-microscope video with AMBF simulation for the navigation of skull base surgery. Surgeons are able to see both AMBF simulation and microscopic view from a VR headset. Additionally, they can change different modes for displaying both videos. In order to view the anatomy from different perspectives, they can rotate, scaling, and slicing the view on the ABMF simulation incorporating with real-time microscopic video to get more detailed information during the operation.  

Overall, we accomplished the basic functionality of the system, but there are still some aspects that need to be optimized. Reducing the latency time is one of the major parts of our project. The current latency time of the system is about 0.3 seconds, but it is not ideal based on our mentor’s feedback, and it needs to be reduced as small as possible so that surgeons satisfied with it. One main reason caused the latency time is our hardware setup: the microscopic video is transmitted from MockOR computer to our laptop by router. If the microscopic video can be directly processed and displayed on the MockOR computer, the latency time of the system could be reduced. This is one of the future works that need to be done for our project. 

There are two windows of videos displayed on the HMD, but the small window does not have an excellent display effect. The view of left and right eyes is not perfectly aligned with each other. This problem should be solved by adjusting the distortion coefficients and window scale parameters. Another aspect of the system that needs to be improved in the future is clarity. The video displayed on the HMD is not as clear as it is on the computer. This problem might be caused by resolution of HMD. Using the higher performance HMD could be one solution.

======Dependencies======
{{ :courses:456:2023:projects:456-2023-13:dependency.png?600 |}}

We have six dependencies for our project. The first four dependencies are the foundation of all works. So, we finish them at the beginning of the semester. Checking hardware is a continuous task because we always need them to work.

For the goals in summer holiday, we need to have IRB approval for user study with surgeons. This dependency is planned to be finished in the beginning of July.

======Milestones and Status ======
  - Milestone name: Set up environment and learn AMBF codes.
    * Planned Date: 2/13/2023
    * Expected Date: 2/16/2023
    * Status: 100%
  - Milestone name: Read the video from stereo microscopic to computer in proper format.
    * Planned Date: 2/20/2023
    * Expected Date: 3/9/2023
    * Status: 100%
  - Milestone name: Process the stereo microscopic video in the computer.
    * Planned Date: 3/10/2023
    * Expected Date: 3/25/2023
    * Status: 100%
  - Milestone name: Minimize the delay of showing videos. 
    * Planned Date: 3/26/2023
    * Expected Date: 4/5/2023
    * Status: 100%
  - Milestone name: Display all videos in HMD.
    * Planned Date: 4/6/2023
    * Expected Date: 4/17/2023
    * Status: 100%
  - Milestone name: Develop an user interface for the system.
    * Planned Date: 4/12/2023
    * Expected Date: 4/20/2023
    * Status: 100%
  - Milestone name: Perform anatomy registration.
    * Planned Date: 4/21/2023
    * Expected Date: 5/10/2023
    * Status: Already finished by optical tracker system, but have not applied on the system
  - Milestone name: Update from the real operation to the simulation.
    * Planned Date: 5/15/2023
    * Expected Date: 8/15/2023
    * Status: Plan to work in summer holiday
  - Milestone name: Conduct user study with surgeons.
    * Planned Date: 5/15/2023
    * Expected Date: 8/15/2023
    * Status: Plan to work in summer holiday

======Timeline======
{{ :courses:456:2023:projects:456-2023-13:timeline.png?600 |}}

According to the timeline we made at the beginning of this semester, we will finish all minimum and expected goals before May 11th and all maximum goals before August 15th.

All minimum and most of the expected goals are finished on time. The only task that we are unable to finish is the registration task. This is because the debugging process of hardware and software takes more time than we expected. We believe we can finish it in one more week after May 11th.

======Reports and presentations======

  * Project Plan
    * {{ :courses:456:2023:projects:456-2023-13:project_plan_presentation.pdf |}}
    * {{ :courses:456:2023:projects:456-2023-13:project_plan_proposals_team13.pdf |}}
  * Project Background Reading 
    * {{ :courses:456:2023:projects:456-2023-13:background_reading_presentation1.pdf |}}
    * {{ :courses:456:2023:projects:456-2023-13:fully_immersive_virtual_reality_for_skull-base.pdf |}}
    * {{ :courses:456:2023:projects:456-2023-13:virtual_reality_for_synergistic_surgical_training_and_data.pdf |}}
    * {{ :courses:456:2023:projects:456-2023-13:twin-s_a_digital_twin_for_skull-base.pdf |}}
  * Project Checkpoint
    * {{ :courses:456:2023:projects:456-2023-13:checkpoint_presentation.pdf |}}
  * Paper Seminar Presentations
    * {{ :courses:456:2023:projects:456-2023-13:background_reading_presentation1.pdf |}}
  * Project Final Presentation
    * {{ :courses:456:2023:projects:456-2023-13:cis2_team13_poster.pdf |}}
  * Project Final Report
    * {{ :courses:456:2023:projects:456-2023-13:cis2_final_report_team_13.pdf |}}
======Project Bibliography=======
[1] Munawar, A., Li, Z., Kunjam, P., Nagururu, N., Ding, A. S., Kazanzides, P., ... &
Unberath, M. (2022). Virtual reality for synergistic surgical training and data generation.
Computer Methods in Biomechanics and Biomedical Engineering: Imaging &
Visualization, 10(4), 366-374.

[2] Shu, H., Liang, R., Li, Z., Goodridge, A., Zhang, X., Ding, H., ... & Unberath, M.
(2022). Twin-S: A Digital Twin for Skull-base Surgery. arXiv preprint
arXiv:2211.11863.

[3] Adnan Munawar, Zhaoshuo Li, Nimesh Nagururu, Danielle Trakimas, Peter
Kazanzides, Russell H. Taylor and Francis X. Creighton. Fully Immersive Virtual Reality
for Skull-base Surgery: Surgical Training and Beyond

[4] Scholz M, Parvin R, Thissen J, Löhnert C, Harders A, Blaeser K. Skull base
approaches in neurosurgery. Head Neck Oncol. 2010 Jul 5;2:16. doi: 10.1186/1758-3284-
2-16. PMID: 20602753; PMCID: PMC2913918.

[5] Locketz GD, Lui JT, Chan S, Salisbury K, Dort JC, Youngblood P, Blevins NH.
Anatomy-Specific Virtual Reality Simulation in Temporal Bone Dissection: Perceived
Utility and Impact on Surgeon Confidence. Otolaryngol Head Neck Surg. 2017
Jun;156(6):1142-1149. doi: 10.1177/0194599817691474. Epub 2017 Mar 21. PMID:
28322125.

[6] Skull base surgery. Skull Base Surgery | Johns Hopkins Medicine. (2019, November
19). Retrieved February 14, 2023, from https://www.hopkinsmedicine.org/health/treatment-tests-and-therapies/skull-base-surgery

[7] Wikimedia Foundation. (2022, July 13). Asynchronous multi-body framework.
Wikipedia. Retrieved February 14, 2023, from https://en.wikipedia.org/wiki/Asynchronous_multi-body_framework

[8] The University of Sheffield. (n.d.). How do you identify the sex of a skull?
FutureLearn. Retrieved February 21, 2023, from https://www.futurelearn.com/info/courses/forensic-facial-reconstruction/0/steps/25656#:~:text=Generally%2C%20male%20skulls%20are%20heavier,the%20sex%20of%20a%20skull.

[9] Bourke, P. (1999, July). Calculating Stereo Pairs. Calculating stereo pairs. Retrieved
February 22, 2023, from http://paulbourke.net/stereographics/stereorender/

[10] Wiki. ros.org. (n.d.). Retrieved February 22, 2023, from
http://wiki.ros.org/image_pipeline

[11] OpenXR - high-performance access to AR and VR -collectively known as XRplatforms and devices. The Khronos Group. (2016, December 6). Retrieved February 22, 2023, from https://www.khronos.org/openxr/

[12] OpenHMD. (n.d.). OpenHMD/openhmd: Free and open source API and drivers for
immersive technology. GitHub. Retrieved February 22, 2023, from https://github.com/OpenHMD/OpenHMD

[13] Yuhas, Daisy. “Speedy Science: How Fast Can You React?” Scientific American,
Scientific American, 24 May 2012, https://www.scientificamerican.com/article/bringscience-home-reaction-time/.
======Documentation======
1. **Github README.md**: https://github.com/jackeyhappie/volumetric_drilling_real_camera#readme

2. **Hardware Setup Manual**:{{ :courses:456:2023:projects:456-2023-13:simulation_assisted_navigation_system_hardware_manual.pdf |}}
courses/456/2023/projects/456-2023-13/project-13.txt · Last modified: 2023/05/11 17:12 by xchen254