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Project report for Tsekos, Lab Reports of Computer Science

University of Houston (UH)Computer Science
Prof. Nikolaos Tsekos

here is the answer for Project report for Tsekos

Typology: Lab Reports

2025/2026

Uploaded on 12/12/2025

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COSC 4372-6370 Medical Imaging
Project Version 1: Virtual X-rays
Project Version 2: Mammography
OVERVIEW: Implement a system to simulate the generation of plain film x-ray. These
are two projects for one person! They are similar and they differ only on the design of
the phantom
Implement the software to simulate a
conventional/standard film x-ray machine
using a GUI to run it. Through this GUI
change the parameters to control data
acquisition, view the reconstructed images
and perform simple analysis. You will use two
phantoms. One is a simple “testing/validation”
2D phantom, and you will use it to test if your
algorithms are working correctly and analyze
the effect of different acquisition parameters.
The second phantom will be a 3D phantom to
simulate a leg or a breast for mammography.
SPECIFICS:
1. Develop the different functions/code to perform all necessary calculations to:
- Generate the phantoms
- Adjust the geometric and the acquisition parameters
- Generate the 1D profile of the 2D phantom and the 2D image for the 3D
phantom
2. Implement a GUI that combines those pieces of code and performs the different
tasks.
3. The control of your x-ray machine will include: the energy of the beam, the x-ray
angle, the distance of the film and the source from the phantom.
Note: when you change the energy you should also change the
µ
values of your
phantom! One simple solution is to use a pull down menu to select ONLY a few
energy values (so you have a small number of tissue values to deal with)
4. Test/validation phantom: Generate the profile of the test phantom and verify that
your algorithms work correctly when:
• Change the distances between source, film and phantom
• Change the values of the two structures.
• Change the angle of the x-ray; what is the effect?
5. Then work with the “human” phantoms.
6. First cerate the phantom in 3D as a 3D matrix:
X-Ray source
Variable
Variable
Variable
Variable angle
X-Ray source
Variable
Variable
Variable
Variable angle
X-Ray source
Variable
Variable
Variable
Variable angle
pf3
pf4
pf5
pf8
pf9

Partial preview of the text

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COSC 4372-6370 Medical Imaging

Project Version 1: Virtual X-rays

Project Version 2: Mammography

OVERVIEW: Implement a system to simulate the generation of plain film x-ray. These are two projects for one person! They are similar and they differ only on the design of the phantom Implement the software to simulate a conventional/standard film x-ray machine using a GUI to run it. Through this GUI change the parameters to control data acquisition, view the reconstructed images and perform simple analysis. You will use two phantoms. One is a simple “testing/validation” 2D phantom, and you will use it to test if your algorithms are working correctly and analyze the effect of different acquisition parameters. The second phantom will be a 3D phantom to simulate a leg or a breast for mammography. SPECIFICS:

  1. Develop the different functions/code to perform all necessary calculations to:
    • Generate the phantoms
    • Adjust the geometric and the acquisition parameters
    • Generate the 1D profile of the 2D phantom and the 2D image for the 3D phantom
  2. Implement a GUI that combines those pieces of code and performs the different tasks.
  3. The control of your x-ray machine will include: the energy of the beam, the x-ray angle, the distance of the film and the source from the phantom. Note: when you change the energy you should also change the μ values of your phantom! One simple solution is to use a pull down menu to select ONLY a few energy values (so you have a small number of tissue values to deal with)
  4. Test/validation phantom: Generate the profile of the test phantom and verify that your algorithms work correctly when:
    • Change the distances between source, film and phantom
    • Change the values of the two structures.
    • Change the angle of the x-ray; what is the effect?
  5. Then work with the “human” phantoms.
  6. First cerate the phantom in 3D as a 3D matrix: X-Ray source Variable Variable Variable Variable angle X-Ray source Variable Variable Variable Variable angle X-Ray source Variable Variable Variable Variable angle
  • Leg project ONLY: The leg phantom will be a cylinder that simulates the leg and another cylinder that simulates the bone
  • The Breast project ONLY: will be a rounded edge 3d structure with a sphere at its center that simulates a cancerous lesion.
  1. Expand your code to generate the 2D image of your 3D phantoms.
  2. For the Leg project ONLY: After you validate that your algorithms works flawlessly, then modify your phantom to simulate a broken leg as shown the figure. Generate the film x-ray image. Test for a split that is orthogonal to the bone and one that is in angle!
  • What is contrast of the split?
  • If it is in an angle what is happening?
  • If you widen the gap of the angled split what do you observe in regard to contrast?
  1. For the Breast project ONLY: After you validate that your algorithms works flawlessly, answer first the question:
  • What is the contrast of the cancerous lesion relative to the rest of the tissue?
  • Can you see clearly the cancer?
  • Now compress the breast by reducing the width of your phantom. What is the effect of this? Quantify the effect you may have X-Ray source Film Variable Variable Variable cone angle^ Angled split Orthogonal split

LEG PHANTOM

X-Ray source Film Variable Variable Variable cone angle^ Angled split Orthogonal split

LEG PHANTOM

COSC 4372-6370 Medical Imaging

Virtual CT scanner

OVERVIEW: Implement a virtual CT scanner and study the effect of changing imaging parameters on the image quality. Implement the software to simulate your scanner on Matlab and use a GUI to run it. Through this GUI you should be able to change the characteristics of your phantom, the parameters to control data acquisition, view the reconstructed images and perform simple analysis. The majority of your work will be performed on “test/validation” phantoms. Those will be simple phantoms like those two in the figure below: a circular one with circular and rectangular structures. You will use those phantoms to study and analyze the effect of different acquisition parameters on image quality. The second phantom will be a head phantom generated with the phantom() function of Matlab. Use this as a final demonstration that your scanner works properly! SPECIFICS:

  1. Develop the different functions/code to perform all necessary calculations for:
    • Generate the phantoms
    • operation of the scanner
    • image reconstruction
    • image analysis
  2. Implement a GUI that combines those pieces of code and performs the different tasks.
  3. Test/validation phantom: a cylinder one with several circular structures of different sizes and the other with a single rectangular structure in the middle (see figures above). From your GUI you should be able to change the matrix size, the dimensions and values of the structures. Note: Assign to each structure values different enough so you can have good contrast differences; after you have your GUI ready just test different combinations.
  4. Head-phantom: Use the phantom() function by Matlab.
  5. Image Analysis: Implement code for three types of image analysis:
  • Signal Intensity (SI) and Contrast (relative signal intensity differences between two regions). These quantities should be reported as numbers and you will use them to investigate whether your calculations are correct (how? e.g. is the beam attenuation correctly calculated?)
  • Image Difference: This will be used to compare your image generated by your scanner and the original input which is your phantom. You will use this type of analysis to identify artifacts or other problems with image reconstruction.
  • Signal Intensity (SI) profiles: Generate graphs of the signal intensity vs. position along a specific direction. You will use those graphs to investigate for potential artifacts. You must be able to compare the profile of both your original object (phantom) and your image (the output of your virtual scanner). So, you can arrange to view two or more profiles in the same figure-graph.
  1. The scanner part of the GUI should allow you to change the different parameters of data acquisition: number of detectors, distance or density of detectors, type of detector array (linear or arc), the distance of the source from the center of the scanner, the step angle of the detector as it goes around the patient. Add a run button to activate the acquisition. In the output do not forget to add appropriate comments that list the parameters you used (Matlab gives you some good options for this)
  2. Using the test/validation phantom investigate the effect of changing acquisition parameters. In all cases the “ground truth” is your original phantom! You will compare the images generated by your code relative to this phantom! Use the different tools in section 5 to investigate how your scanner works. Compare the image and the validation phantom for different acquisition parameters:
  • What is the effect of increasing the step of the rotation angle?
  • What is the effect of reducing the number or the distance of the detectors?
  • In the phantom with the circular structures, what is the effect on them?
  • How are the edges of the rectangular structure I the second phantom appear in the image? Any improvements?
  • What is the overall image impression? What may cause this phenomenon?
  • What parameters give you the best possible image?
  • Add a time parameter and (e.g. the duration of data acquisition per rotation) and investigate how “the longer the acquisition time the better the collected images”

SPECIFICS:

  1. Develop the different functions/code to perform all necessary calculations for:
    • Generate the phantoms and their corresponding k-space
    • operation of the scanner by selecting different acquisition schemes
    • sample the data with a specific trajectory
    • image reconstruction
    • image analysis
  2. Implement a GUI that combines those pieces of code and performs the different tasks.
  3. Test/validation phantoms: From this GUI you should be able to change the matrix size and the dimensions of those embedded structures.
  4. Systematically study your code using the two phantoms. Suggestion: make the phantom with very high resolution 4Kx4K matrix size, this will give you a better results. Why?
  5. For this project you will ignore T1, T2 effects. You will assume that your TR is infinity and your TE is zero.
  6. Image Analysis: Implement code for three types of image analysis:
    • Signal Intensity (SI) and Contrast (relative signal intensity differences between two regions). These quantities should be reported as numbers and you will use them to investigate whether your calculations are correct (how? e.g. is the beam attenuation correctly calculated?)
    • Signal Intensity (SI) profiles: Generate graphs of the signal intensity vs. position along a specific direction. You will use those graphs to investigate for potential artifacts. You must be able to compare the profile of both your original object (phantom) and your image (the output of your virtual scanner). So, you can arrange to view two or more profiles in the same figure-graph.
  7. The scanner part of the GUI should allow you to change the different acquisition schemes (a simple solution is with pull down menus). Add a run button to activate the acquisition. In the output do not forget to add appropriate comments that list the parameters you used (Matlab gives you some good options for this)
  8. Using the test/validation phantom investigate the effect of changing acquisition parameters. In all cases the “ground truth” is your original phantom! You will compare the images generated by your code relative to this phantom! Use the different tools in section 5 to investigate how your scanner works. Compare the image and the validation phantom for different acquisition parameters:
    • How the edges of the rectangular structure the first phantom are appear in the image? Any improvements?
    • In the phantom with the circular structures, what is the effect on them?
    • What is the overall image impression?
    • What parameters give you the best possible image?
    • Add a time parameter and (e.g. this will be the duration of data acquisition per horizontal line for the Cartesian acquisition, and per radial line for the radial acquisition) and investigate how “the longer the acquisition time the better the collected images”

COSC 4372-6370 Medical Imaging

Virtual simulation of Angio- and Perfusion MRI

OVERVIEW: The purpose o your project is to implement a model of tissue that simulates angiography and perfusion and image it with contrast enhanced MRI using an exogenous contrast agent. Assume that this agent reduces the T1 of tissue and you are using a T1-weighted MRI protocol (so the agent will increase the signal intensity – SI- of tissue). Figure 1 shows a model of a heart. Phantom: Figure 1 shows the phantom that will have the following features (note that those are simplifications of what is actually happening in the real tissue):

  • The phantom does NOT move (it does not simulate cardiac beating) and will have two compartments, one representing tissue with normal perfusion and the other with abnormal perfusion.
  • In the part with normal perfusion the blood (+ agent) enters and then leaves without returning again.
  • The part with abnormal perfusion will have two characteristics: the blood will enter slower than in this of normal tissue and then it will come back again and accumulate there (i.e. stay!)
  • Before the injection of the contrast agent assume that the tissue has a signal of 1.0 and the background 9empty space) is 0.0 (as shown in figure 2) Tissue characteristics: Output: This side has normal perfusion This side has abnormal perfusion Blood feeding arteries Figure 1: the phantom Figure 2: The image frame relative to the phantom. Assign 0. signal to the “empty” space. This side has normal perfusion This side has abnormal perfusion Blood feeding arteries This side has normal perfusion This side has abnormal perfusion Blood feeding arteries Figure 1: the phantom Figure 2: The image frame relative to the phantom. Assign 0. signal to the “empty” space.