Software Manual

Management & Post Processing of Prostate MRI Images Post-Processing

Saad Masood, A.S.M.Shiahvuddin & Muhammad Habib Mahmood

1. Functional Block Diagram am

Figure.1

Figure.1. Figure.1 Functional Block Diagram 2. How to Run the Program

The steps which are needed to be followed for the program to execute and to be used are as stated as under. Every function along with its required steps is described. Run the Program

Figure.2

First make sure that all the files listed below are included in one directory. Open the file Med_IM.m and Run it. Click Change Directory if prompted. The window showed in Figure.X should appear. Problem: If the program does not run, there is a problem with the code. This is not the right file, contact the concerned group. Figure.3

Load Patient

In the main console window, there is a tab on the bottom left side Load Patient. Press it. Now in the browser window, browse to the path where the patients *.rda file is located.

Figure.4

Condition: The folder containing the *.rda file should contain all the images in their respective folders. o Folder 3D T2 for 3D T2 weighted DICOM images

o Folder ADC for Diffusion DICOM images o Folder Perfusion for Perfusion DICOM images
For example: In the folder Patient 291, the file Patient.rda is present. This file is browsed through the Load Patient browser. This folder contains three folders 3D T2, ADC & Perfusion. All these folders contain their respective DICOM Images. Once the *.rda file is browsed, the respective patient information appears on the bottom left corner of the main console window.

Load Images
There is a Load images tab on the centre right side of the main window. This tab is used to load different kind of DICOM Images. On the top right side there are three check boxes against each type of DICOM image to be loaded. When any of the check box is checked and the Load Images tab is pressed the respective images are displayed on the left side of the main window. By default, for every type of image, the first image present in the folder is displayed. Figure.5

For example: 3D T2 Images check box is checked and the Load Images tab is pressed. Then the image named image00001 from the 3D T2 folder is displayed as shown in Figure.X. The same happens when Diffusion images and Perfusion Images check boxes are checked.

Layer
There are three layers in display. Image Layer It is the image which is currently on display. Whenever any of the three types of images 3D T2 Images, Perfusion & Diffusion are selected and loaded, the Image layer is active and it changes whenever there is a change in Image display by scrolling or zooming. If it is remained unchecked, the display would freeze to the last displayed image. It again refreshes when the Image Layer is checked again.

Figure.6

Grid Layer It is the spectroscopic grid identified by the *.rda file for the current patient. If this check box is checked the grid is shown on top of the image layer. If it is not checked, the grid layer would become inactive and it will not be shown in the display. This is shown in Figure.X and Figure.X respectively. Figure.7

Characterization Layer It is the voxel/voxels in the grid which have been selected and characterized. If this is checked, whenever the selected voxels appear on the display, they will be shown in green boxes and if it is not checked, the voxels all the voxels would appear the same.

Image Slice
This appears on the lower left side of the main window. It refers to the image number which is currently being displayed in the display window. This is in accordance with the name of the file i.e. the file named image0001 is shown as Image Slice number 1.

Grid Slice
This too appears on the lower left side of the main window. It refers to the slice of the spectroscopic grid which is currently on display. A Grid Slice spans over 2 to 5 Image Slice depending on the type of images being displayed. When the Image Slice does not coincide with any Grid Slice, the Grid Slice box remains empty.

UI Selections
The User Interface Selections can perform three operations. Amongst these operations only one can be performed at each time. These are given below Zoom When this selection is made, the image on display can be zoomed in or zoomed out. To zoom in place the mouse pointer on the place where zooming in is required and click left mouse button. To zoom out place the mouse pointer on the place where zooming out is required and click right mouse button. It should be remembered that selection of voxels cannot be made on the zoomed image. For selection, the image should be displayed in its original size. To go back to the original size, press Shift and click left mouse button anywhere on the image. The zoomed image of the white dashed square box in Figure.X is shown in Figure.X Figure.8

Scrolling When this selection is made, the Up and Down tabs shown alongside the displayed image come into use. On clicking Up the images next to the displayed imaged is displayed and when the Down tab is pressed, the image previous to the displayed image is displayed. It can be observed here that as the Up and Down buttons are pressed, the respective image slice number is updated in the Image Slice box. The Grid Slice number changes according to the Image Slice being displayed. Selection When this tab is selected, then it means that no more scrolling is required and that a selection of voxels can be done. Selection can be done as Single or Multiple voxels.

Single voxel selection is done by first selecting the Selection check box and then selecting Single from the drop down list. Here Grid Layer should be checked to see the spectroscopic grid as all the selections are done in the voxels spanned by the spectroscopic grid. On clicking on a voxel, the small square red box indicating the voxel turns green. This means that the voxel has been selected. This selected voxel can be characterized in case of 3D T2 Images and Diffusion Images. The characterization is done by selecting the check boxes of Left or Right for L/R Characterization, Central or Peripheral for Zone Characterization and Apex, Median or Base for Position Characterization. As soon as the check box is selected, the Region label and the corresponding Mean is automatically assigned to the selected voxel. Figure.9

Multiple voxel selection is done by first selecting the Selection check box and then selecting Multiple from the drop down list. Here Grid Layer should be checked to see the spectroscopic grid as well. On clicking on a voxel, the small square red box indicating the voxel turns green. This means that the voxel has been selected. Similarly any number of voxels on the same grid can be selected, when the selection is complete click the right mouse button, indicating that you have finished selection and now you want to characterize. These selected voxels again can be characterized in case of 3D T2 Images and Diffusion Images. The characterization is done by selecting the check boxes of Left or Right for L/R Characterization, Central or Peripheral for Zone Characterization and Apex, Median or Base for Position Characterization. As soon as the check box is selected, the Region label and the corresponding Mean is automatically assigned to the selected voxel. For Perfusion images, the selection is done in the same manner but the characterization is not possible, as these are images over time. Any selection can be selected again by clicking Left Mouse Button on top of the selected voxels, and the characterization done for that region would appear on the lower right hand side. If the Reject Button is pressed, the selection is deleted and then it no more exists. The region labels assigned to the selection on each Grid Slice start from one.

Figure.10

Figure.11

Export to Excel
Depending on the type of Images which has been selected, Export to Excel button will write the corresponding characterization Structure to the *.xls file. For 3D T2 images, Characterization_3D_T2 is written For Diffusion images, Characterization_Diffusion is written For Perfusion images, Characterization_Perfusion is written and for the evaluation over time Perfusion_Curve is written

All the files are written on the path where the *.rda file was browsed. The files should be renamed or cut before, exporting another excel file from the software. In the excel files, data from each slice is written on each sheet for easy readability. The software cannot read the excel files, to perform evaluation of the same set of regions in a later session.

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Open Figure
When the user wants to see the wash-in/wash-out curve of any region on perfusion images, the Open Figure button should be pressed. This would open a blank plot window. On selecting the region of which the wash-in/wash-out gradient is required, the plot will appear on the plot window, with the gradient of each shown. The value of the gradient is displayed on the corresponding data boxes of Gradient_Wash-in and Gradient_Wash-out. Figure.13

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3. Samples
Display 3DT2 Images
Click Load Patient Load *.rda file Check 3DT2 Images Click Load Images Check image Layer, Grid Layer and Characterization Layer Check Zooming Right/Left Click on the displayed image to Zoom in/Zoom out Press Shift on keyboard and Click anywhere on the displayed image to return to original size. Check Scrolling Press Up and Down to scroll through Image Slice Grid layer is on, so observe the Grid Slices which have different Images Check Selection Select Single Make a selection of voxel on the grid on any layer, characterize it and Submit