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courses:446:2013:446-2013-1:ultrasound_imaging_of_brain_shunts [2013/05/06 15:05]
rhan3@johnshopkins.edu [Technical Approach]
courses:446:2013:446-2013-1:ultrasound_imaging_of_brain_shunts [2019/08/07 12:01] (current)
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 ======Ultrasound Imaging of Brain Shunts====== ======Ultrasound Imaging of Brain Shunts======
-**Last updated: ​28/02/2013 14:19pm**+**Last updated: ​6/05/2013 16:09pm**
  
  
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 ======Deliverables====== ======Deliverables======
    
-  * **Minimum:​** (03/​26/​2013)+  * **Minimum:​** (03/​26/​2013) ​--Achieved
     - An ultrasound friendly brain phantom is designed and built, with shunts inserted. ​     - An ultrasound friendly brain phantom is designed and built, with shunts inserted. ​
-    - Laser and US system is tested preliminarily for PA signal detection with tissue-like material. ​-- Done +    - Laser and US system is tested preliminarily for PA signal detection with tissue-like material. 
-    - Experiment data is collected and processed without skull to form delayed images. ​--Done +    - Experiment data is collected and processed without skull to form delayed images. 
-    - Experiments with different distance between the end of fiber and the occlusion is conducted. ​--Working on +    - Experiments with different distance between the end of fiber and the occlusion is conducted.
-    - More to be added and updated+
  
-  * **Expected:​** (04/​20/​2013) +  * **Expected:​** (04/​20/​2013) ​--Achieved 
-    - Experiment data with skull is collected and processed. ​+    - Experiment data with skull is collected and processed. Pig pelvis bone is used.
     - Different levels of occlusion can be recognized from the image. ​     - Different levels of occlusion can be recognized from the image. ​
-    - Shunts, tissues and fluid will be able to distinguish. +    - <del>Shunts, tissues and fluid will be able to distinguish.</​del> ​-- They are all nearly transparent with the ultrasound.
-    ​More to be added and updated+
  
-  * **Maximum:​** (05/​10/​2013) +  * **Maximum:​** (05/​10/​2013) --Achieved 
-    ​Faster image processing method is developed. +    - <del>Real-time imaging through the skull for occlusion and shunts is achieved.</​del>​ Changed to delayed imaging due to limitation of the data collecting and processing time of the hardware(DAQ).  
-    - Real-time imaging through the skull for occlusion and shunts is achieved.  +    - <del>Monitor the clearing ​procedure of the shunt.</​del>​ Changed ​to the visualization of the approaching process of the fiber end point to occlusion, ​and the accumulation process of the occlusion. 
-    - Monitor the surgery ​procedure of clearing ​the shunt. +(Version ​3)
-    - More to be addd and updated +
-(Version ​1)+
 ======Technical Approach====== ======Technical Approach======
 \\ \\
 +**<fs large>​Proposed Solution</​fs>​**\\
 +In order to conquer this weakness that ultrasound cannot penetrate skull, photoacoustic imaging technique is used. To generate photoacoustic effect, laser system is integrated with the ultrasound system.\\
 +
 +**Working Principle Specification:​**\\
 +A high frequency pulses of light is launched onto the occlusion. The energy of the light absorbed by the occlusion will convert into heat, which makes the molecules become thermally excited. Then, the pressure variations caused by radiation of the heat will propagate as ultrasound waves in the occlusion. So that it can be detected by ultrasound probe.\\
 +
 +{{ :​courses:​446:​2013:​446-2013-1:​working_priciple.png?​direct&​300 |}}\\
 +
 +
 +**<fs large>​Feasibility Demonstration of The Proposed Solution</​fs>​**\\
 +
 **<fs larger>​Phantom Construction</​fs>​**\\ **<fs larger>​Phantom Construction</​fs>​**\\
  
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   -The PVA solution is cooled to -17 degree Celsius for about 12 hours. ​   -The PVA solution is cooled to -17 degree Celsius for about 12 hours. ​
   -The solution warms back to room temperature in a continuous way for another 12 hours. ​   -The solution warms back to room temperature in a continuous way for another 12 hours. ​
-Step 1. to 4. is a whole F/T cycle. If needed, this F/T cycle can be repeated for several times. Without the addition of dimethyl sufoxide, the scattering coefficient will increase with each cycle and the phantom will be stiffer, too. \\+Step 1. to 4. is a whole F/T cycle. If needed, this F/T cycle can be repeated for several times. Without the addition of dimethyl sufoxide, the scattering coefficient will increase with each cycle and the phantom will be stiffer, too. The figure below is one of the phantoms we created.\\ 
 + 
 +{{ :​courses:​446:​2013:​446-2013-1:​brain_phantom.png?​direct&​300 |}}
  
 For the skull part, we proposed a construction process here. But we finally choose to use fresh bones for the experiment because the unavailability of the specific type 3D printer.\\ For the skull part, we proposed a construction process here. But we finally choose to use fresh bones for the experiment because the unavailability of the specific type 3D printer.\\
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   -Prototyping (Powder-binder combination:​ ZP130TM and ZB58TM; 3D printer: Z510TM Spectrum)   -Prototyping (Powder-binder combination:​ ZP130TM and ZB58TM; 3D printer: Z510TM Spectrum)
   -Post-processing:​ cleaning, support removal, infiltration,​ etc.    -Post-processing:​ cleaning, support removal, infiltration,​ etc. 
-In step 6., the infiltration is performed by immersion under vacuum conditions in a dedicated chamber. The samples were maintained at -95kPa for min, at the temperature of 25°C. Then, the atmospheric inlet valve is opened to relieve the vacuum, causing a further penetration of the infiltrant by atmospheric pressure action. Finally, the samples are extracted from the chamber and the excess resin is wiped off the surface.+In step 6., the infiltration is performed by immersion under vacuum conditions in a dedicated chamber. The samples were maintained at -95kPa for min, at the temperature of 25°C. Then, the atmospheric inlet valve is opened to relieve the vacuum, causing a further penetration of the infiltrant by atmospheric pressure action. Finally, the samples are extracted from the chamber and the excess resin is wiped off the surface.\\ 
 +The image below is the snotshot of the 3D Model we created in the Solidworks.\\
  
 +{{ :​courses:​446:​2013:​446-2013-1:​skull_model_1.png?​direct&​300 |}}\\
  
 +**<fs larger>​System Setup</​fs>​**\\
 +The Photoaoustic Laser System of OPOTEK Inc. has been used to project pulses at 1064nm wavelength into a fiber of 1mm diameter, which has been inserted into the shunts with its tip directly pointing to the occlusion material. SonixTouch ultrasound system, developed by Ultrasonix Medical Corporation (Richmond, Canada), was used to detect the excited acoustic waves, together with a transducer probe placed right on top of the phantom. The Sonix DAQ device, jointly developed by the University of Hong Kong and Ultrasonix, was used to collect the pre-beamformed radiofrequency (RF) data from the US machine into .daq files. Finally, those .daq files are processed with MATLAB to get the beamformed image.\\
 +{{ :​courses:​446:​2013:​446-2013-1:​system_setup2.png?​direct |}}
  
 +**<fs larger>​Experimental Setup</​fs>​**\\
 +A shunts mimicking plastic tube containing water and occlusion has been inserted into the brain phantom horizontally. The transducer probe has been put in aligned with the shunt. Figure 7 shows a B-mode ultrasound image of the shunts inside the phantom, with fiber and occlusion inserted. Though we cannot see the fiber and the occlusion in the shunts clearly, their positions can be decided by the shadows they have created below them.\\
  
 +{{ :​courses:​446:​2013:​446-2013-1:​experiment_setup.png?​direct&​300 |}}\\
  
 +High attenuation jello-based material has been used to mimic the occlusion. Nova of Ophir Optronics has been used as the laser energy/​power meter. Energy between 0.7mJ/cm2 to 1.5mJ/cm2 at the fiber end tip has been adopted for the experiments,​ which is much lower than the maximum allowable energy of 30mJ/cm2 exposed on tissue according to the ISO laser safety standards. A limitation of our occlusion material is that it will get burnt when the laser energy is over 1mJ/cm2, and no signal will be generated after that. A brachytherapy seed has been put right before the occlusion material to prevent this situation when high energy is needed in the experiments of visualization of the fiber end point. The occlusion at the end of the shunt is used to prevent water from leaking out, which is far out of the FOV.\\
  
-(Version ​2)+{{ :​courses:​446:​2013:​446-2013-1:​shunt_with_water.png?​direct&​300 |}} 
 + 
 +Different sizes of the occlusion material have been prepared for imaging in Figure.. The thickness is halved for the second occlusion.\\ 
 + 
 +{{ :​courses:​446:​2013:​446-2013-1:​different_sizes_occlusion.png?​direct&​300 |}} 
 + 
 +To mimic human skull, a fresh pig pelvis bone has been cut and shaved into two pieces of different thickness, 2mm and 4mm. Then, one of the two pieces has been inserted between the phantom and the transducer probe.\\ 
 +In the experiments to visualize fiber end point, a metal needle has been tied up together with the fiber, and a piece of occlusion material has been put at the end of the needle. The acoustic wave generated by the seed and the occlusion will be reflected by that piece of occlusion material, so the position of the fiber end point can be seen in PA images.\\ 
 + 
 +{{ :​courses:​446:​2013:​446-2013-1:​fiber.png?​direct&​300 |}} 
 + 
 +To mimic the reversed process of clearing the shunts, occlusion material has been cut into tiny pieces and mixed with ultrasound jell to put into a injection syringe and inject into the shunts. Therefore, visualization of the accumulation of the occlusion could be achieved.\\ 
 + 
 +{{ :​courses:​446:​2013:​446-2013-1:​syringe_with_tiny_occlusion.png?​direct&​300 |}} 
 + 
 +(Version ​3)
 ======Dependencies====== ======Dependencies======
  ​**Dependency:​ Access to Dr. Boctor’s lab and equipment**  ​**Dependency:​ Access to Dr. Boctor’s lab and equipment**
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     - 2. Search on the internet for the cheap brain models     - 2. Search on the internet for the cheap brain models
     - Resolve By: 2/28/2013     - Resolve By: 2/28/2013
-    - Resolved: ​No +    - Resolved: ​Yes 
-    - Status: We have investigated the materials and construction method for both the inner side and the outer side part. A short report will be done by 2/26/2013. Then discussion will be made with Dr. Boctor. ​+
     - Fallback Plan: Beg Dr. Taylor for money to buy a professional model from elsewhere     - Fallback Plan: Beg Dr. Taylor for money to buy a professional model from elsewhere
     - Affects: Milestone 1     - Affects: Milestone 1
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     - Resolution Plan: Dr. Boctor has offered his PhD students to help us     - Resolution Plan: Dr. Boctor has offered his PhD students to help us
     - Resolve By: 5/1/2013     - Resolve By: 5/1/2013
-    - Resolved: ​No+    - Resolved: ​Yes
     - Fallback Plan: give up the maximum deliverables     - Fallback Plan: give up the maximum deliverables
     - Affects: Maximum Deliverables     - Affects: Maximum Deliverables
- ​**Dependency:​ Monitor the real-time ​clearing of brain shunts**+ ​**Dependency:​ Monitor the delayed ​clearing ​procedure ​of brain shunts**
     - Resolution Plan: the clearing stem is built by the company     - Resolution Plan: the clearing stem is built by the company
     - Resolve By: 5/1/2013     - Resolve By: 5/1/2013
-    - Resolved: ​No+    - Resolved: ​Yes
     - Fallback Plan: give up the second maximum deliverable     - Fallback Plan: give up the second maximum deliverable
     - Affects: Maximum Deliverables     - Affects: Maximum Deliverables
  
-(Version ​1)+(Version ​2)
  
 ======Milestones and Status ====== ======Milestones and Status ======
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     * Planned Date:  02/28/2013     * Planned Date:  02/28/2013
     * Expected Date: 04/08/2013     * Expected Date: 04/08/2013
-    * Status: ​Simple shape brain phantoms have been constructed. Next is to get a piece of skull or 3D print one.+    * Status: ​Done
     * {{:​courses:​446:​2013:​446-2013-1:​a_short_report_for_phantom_investigation_v2.pdf| Phantom Material Investigation Report}}     * {{:​courses:​446:​2013:​446-2013-1:​a_short_report_for_phantom_investigation_v2.pdf| Phantom Material Investigation Report}}
   - Milestone name:  Preliminary test of US probe and laser will be completed   - Milestone name:  Preliminary test of US probe and laser will be completed
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     * Planned Date:  04/15/2013     * Planned Date:  04/15/2013
     * Expected Date: 04/22/2013     * Expected Date: 04/22/2013
-    * Status: ​Looking for bone.+    * Status: ​Done
   - Milestone name:  Delayed monitoring for occlusion in shunts through skull will be achieved   - Milestone name:  Delayed monitoring for occlusion in shunts through skull will be achieved
     * Planned Date:  05/10/2013     * Planned Date:  05/10/2013
     * Expected Date: 05/10/2013     * Expected Date: 05/10/2013
-    * Status: ​Not started but planning+    * Status: ​Done
  
-(Version ​2)+(Version ​3)
 ======Reports and presentations====== ======Reports and presentations======
  
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   * Project Checkpoint   * Project Checkpoint
     * {{:​courses:​446:​2013:​446-2013-1:​checkpoint_presentation.pdf| Project checkpoint presentation}}     * {{:​courses:​446:​2013:​446-2013-1:​checkpoint_presentation.pdf| Project checkpoint presentation}}
 +    * {{:​courses:​446:​2013:​446-2013-1:​quick_checkpoint_presentation.pdf| Project quick checkpoint presentation}}
   * Paper Seminar Presentations   * Paper Seminar Presentations
     * Yang Hong     * Yang Hong
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         * {{:​courses:​446:​2013:​446-2013-1:​Paper2_han.pdf| Paper II}}         * {{:​courses:​446:​2013:​446-2013-1:​Paper2_han.pdf| Paper II}}
   * Project Final Presentation   * Project Final Presentation
-    * {{:​courses:​446:​2013:​446-2013-X:final_poster_pdf.pdf|PDF of Poster}}+    * {{:​courses:​446:​2013:​446-2013-1:final_project_poster.pdf|PDF of Poster}}
   * Project Final Report   * Project Final Report
-    * {{:​courses:​446:​2013:​446-2013-X:final_report.pdf|Final Report}}+    * {{:​courses:​446:​2013:​446-2013-1:final_report_v2.pdf|Final Report}}
     * links to any appendices or other material     * links to any appendices or other material
 ======Project Bibliography======= ======Project Bibliography=======
- * here list references ​and reading material+[1]. Sean Jy-Shyang Chen, Pierre Hellier, Jean-Yvs Gauvrit, Maud Marchal, Xavier Morandi, and D. Louis Collins, An Anthropomorphic Polyvinyl Alcohol Triple Modality Brain Phantom based on Colin27, Mechanical Image Computer-Assisted Intervention – MICCAI 2010 6362 (2010) 92-100.\\ 
 +[2]. Fre ́ de ́ ric Bevilacqua, Dominique Piguet, Pierre Marquet, Jeffrey D. Gross, Bruce J. Tromberg, and Christian Depeursinge:​ In vivo local determination of tissue optical properties: applications to human brain. 1 August 1999/ Vol.38, No.22/ Applied Optics.\\ 
 +[3]. Matteo Gatto, Gianluca Memoli, Adam Shaw, Neelaksh Sadhooo, Pierre Gelat, Russell A. Harris, Three-Dimensional Prinrting (3DP) of neonatal head phantom for ultrasound: Thermocouple embedding and simulation of bone, Medical Engineering &​Physics 34 (2012) 929-937.\\ 
 +[4]. Limng Nie, Xin Cai, Konstantin Maslov, ​ Alejandro Garcia-Uribe,​ Mark A.  Anastasio, Lihong V. Wang, “Photoacoustic tomography through a whole adult human skull with a photon recycler”,​ Washington University, Department of Biomedical Engineering,​ St. Louis, Missouri 63130.\\ 
 +[5]. H. J. Kang et al., “Software framework of a real-time pre-beam-formed RF data acquisition of an ultrasound research scanner,” Proc. SPIE 8320, 83201F (2012).\\ 
 +[6]. N. Kuo, H.J. Kang, D.Y. Song, J.U. Kang, E.M. Boctor, "​Real-time Photoacoustic Imaging of Prostate Brachytherapy Seeds Using a Clinical Ultrasound System",​ Journal of Biomedical Optics, 17(6), June 2012.\\ 
 +[7]. P. J. Stolka, ​ H.-J. Kang,  and M. B. Emad, “The MUSiiC toolkit: ​ Modular Real-Time Toolkit for Advanced Ultrasound Research,​” MIDAS Journal, (2010)\\ 
 +[8]. H.-J. Kang, P. J. Stolka, and M.B.Emad, “OpenITGLinkMUSiiC toolkit: A Standard Communications Protocol for Advanced Ultrasound Research,​” MIDAS Journal, (2010)\\ 
 +[9]. M. Fink, “Time reversal of ultrasonic fields-Part I: Basic principles”. IEEE Trans. Sonics Ultrason. 39(5), 555–566 (1992).\\ 
 +[10]. J.-L. Robert, M. Burcher, C. Cohen-Bacrie,​ and M.Fink, “Time reversal operator decomposition with focused transmission ​and robustness to speckle noise: Application to microcalcification detection”. J. Acoust. Soc. Am., 119:​3848-3859 (2006). 
 + 
  
 ======Other Resources and Project Files====== ======Other Resources and Project Files======
-Here give list of other project files (e.g., source ​code) associated with the project. ​ If these are online give a link to an appropriate external repository or to uploaded media files under this name space.+* Project MATLAB beamforming code 
 +    * {{:​courses:​446:​2013:​446-2013-1:​matlab.zip| MATLAB beam-forming ​code}} 
courses/446/2013/446-2013-1/ultrasound_imaging_of_brain_shunts.1367867116.txt.gz · Last modified: 2019/08/07 12:05 (external edit)




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