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MIPT-Oulu · Aug 16, 2022 · 62e17b9 · 62e17b9
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@@ -49,9 +49,35 @@ The virtual object for simulations must be loaded before actual simulation can b
 
 ### X-ray Spectrum
 
-The X-ray spectrum which is utilized in the simulation can be created by clicking the "Generate spectrum" button. The Spectrum tool will then appear on the screen where user can create the desired X-ray spectrum. First, the user must set the X-ray tube settings (kV, exposure, filtration). These parameters allow user to influence the shape of the simulated spectrum. After setting the parameters by pressing the "Generate Spectrum" button, the polychromatic X-ray spectrum will then appear in the figure of the Spectrum tool. The x-axis of the spectrum indicates the energy range of the detected X-ray photons in kiloelectronvolts (keV) and the y-axis the number of obtained X-ray photons per exposure (mAs). spectrum can be also saved by pressing the "Save" button of the Spectrum tool. -->
+The X-ray spectrum which is utilized in the simulation can be created by clicking the "Generate spectrum" button. The Spectrum tool will then appear on the screen where user can create the desired X-ray spectrum. First, the user must set the X-ray tube settings (kV, exposure, filtration). These parameters allow user to influence the shape of the simulated spectrum. After setting the parameters by pressing the "Generate Spectrum" button, the polychromatic X-ray spectrum will then appear in the figure of the Spectrum tool. The x-axis of the spectrum indicates the energy range of the detected X-ray photons in kiloelectronvolts (keV) and the y-axis the number of obtained X-ray photons per exposure (mAs). spectrum can be also saved by pressing the "Save" button of the Spectrum tool. 
+
+### Reconstruction Algorithm
+
+The algorithm for the image reconstruction can be selected by clicking the "Reconstruction algorithm" button. This will open a window with a dropdown menu offering a few options. In addition to Filtered Backprojection (FBP), the user can select the least squares, or Tikhonov Regularization algorithm to be used for image reconstruction.
+
+### Scan geometry
+
+The projection geometry, used in the virtual CT scan, can be selected by clicking the “Projection geometry” button. A window will then open, where the dropdown menu offers user two options for the projection geometry, parallel and fanflat geometries. 
+ 
+### Scan parameters
+
+After selecting the projection geometry, the desired imaging parameters must be set for the simulation. Click the "Imaging parameters" button to open the "Parameter settings", where you can set the parameters required for your simulation (Figure 8). Each parameter has a default value, so you do not need to change the values if it is not necessary for the simulation. When you change the values, you can individually set the values for the projection angle, image volume, detector width, detector element size, tube current, scan time and image noise. The angle parameters represent the minimum and maximum angle of the virtual scan and the angle step the size between the obtained projections. The volume of the image indicates the reconstruction volume. The detector parameters represent the horizontal width of the detector and the one detector element size. Noise naturally represents the amount of noise detected during the scan. With certain settings, you must set values for additional parameters. If you select Tikhonov regularization as the reconstruction algorithm, the settings also ask for the value of the regularization parameter. If you select the gradient descent algorithm, you must also set the step size of the algorithm. Also, if you selected the least squares or gradient descent algorithm, you will need to adjust the number of iterations for the algorithms. In addition, if you have selected "fanflat" as the projection geometry, you will need to adjust the source-to-origin (SOD) and origin-to-detector distances (ODD).
+
+### Virtual CT Scan
+
+Once all imaging parameters are adjusted and projection geometry, X-ray spectrum, and reconstruction algorithm selected, a virtual CT scan can be performed to obtain the projection data (Figure 9). Do this by clicking the "Scan projections" button, and the detection of CT projections with the adjusted settings will begin. When the virtual scan is complete, you can view the sinogram of the received projections by pressing the "Visualize projections" button.
+
+### Reconstruction
+
+After the virtual scan, the reconstruction of the obtained data can be calculated with chosen algorithm by clicking the “Reconstruction” button (Figure 9). The result of the polychromatic reconstruction appears in the left image window of the console and the “Reconstruction Intensities Figure” illustrates the grayscale intensity range of the obtained reconstruction. You can perform a new simulation by pressing the “Load Phantom” button again.
+
+The contrast of the reconstructed image can be adjusted by using the “Contrast panel” sliders (located at the right side of the “Spectral reconstruction” window). To change the contrast of specific reconstruction, select one of the "check box" options, either “polychromatic or spectral reconstruction”, as active.
+
+### Spectral Reconstruction
+
+Calculating the polychromatic reconstruction with FBP algorithm releases the “Spectral parameters” button (CTlab does not allow this feature with other algorithms). With “Spectral parameters” button, user can adjust the energy interval of X-ray spectrum which is utilized in the spectral imaging as well as the number of energy bins included in the energy interval. To adjust the spectral parameters, click the “Spectral parameters” button (Figure 10). After adjusting spectral parameters, spectrum is now divided into different energy bins by dashed lines (illustrated in “X-ray Spectrum Figure”). By pressing the Visualize spectral images button, program starts to calculate reconstructions related to different bins with FBP algorithm. The progress of the spectral reconstruction is reflected in the updated blocks in the “X-ray spectrum Figure” which represent the calculated energy bins. Once the calculation is completed, you will be able to scroll through the spectral reconstructions by using the spinner tool of the “Simulation control panel” (the bin’s energy range is also updated in the top of the spectral window). You can now compare images at different energy bins to the result of the polychromatic FBP reconstruction and analyze how the image quality and the contrast of the materials changes between spectral images (Figure 11). A new simulation can be started by pressing the "Load phantom" button.
+-->
 
-### 
 
 ## Documentation