6 Image Display and Analysis

Chapter 6
Image Display and Analysis

MRiLab incorporated a set of image display and analysis tools. They are designed using Matlab GUIDE, and carefully tuned for manipulating multi-dimensional image data in Matlab.

6.1 MagicRightClick

The user can right click on any MRiLab graphical axes to create an individual figure with the identical graphical content.

6.2 MatrixUser

MRiLab incorporated a toolbox called ‘MatrixUser’ for performing image display and analysis. This toolbox can be activated by pressing ‘MatrixUser’ toolbar icon located at the top of the main simulation console.

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Figure 6.1: MatrixUser Toolbar Icon

MatrixUser will search through the current output folder and load all image series from this folder into Matlab base workspace. The MatrixUser main window (Figure 6.2) works as a matrix manager for loaded images. The user can choose to display image series by using the pop-up menu. The matrix size, type and value range are calculated and provided on the right side. The user can press ‘MatrixUser’ button to activate MatrixUser display window. Current MatrixUser version supports displaying any valid Matlab multi-dimensional matrix and Matlab structure variable.

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Figure 6.2: MatrixUser Main Window

6.2.1 Data Import

By default, MatrixUser reads Matlab base workspace, scans existing matrices in the Matlab session, then creates a matrix list for tracking matrix content. Once those matrices are updated by the user, MatrixUser will also update the matrix list. Moreover, there are several different approaches to import data from outside Matlab into MatrixUser. The imported matrices will be saved into Matlab base workspace. The import functions are located under ‘Load’ menu, including:

Load MAT file
The default Matlab .mat file is natively supported by MatrixUser.
Load System Clipboard
If image content exists in the system clipboard, it can be converted into a RGB image which contains a three slice matrix with each slice corresponds to an individual Red, Green and Blue channel.
Load ScreenShot
MatrixUser takes a full screenshot for current monitor and saves it into a RGB image as described above.
Load from Binary file
Binary data file is supported by MatrixUser. The user needs to properly configure loading parameters (Figure 6.3) according to the matrix size and data type information.

Figure 6.3: MatrixUser Binary File Loading Interface
Load DICOM file(s)
MatrixUser supports loading multiple DICOM files by using a file filter interface (Figure 6.4). The user needs to load DICOM files into the loading interface by selecting desired DICOM files (multiple selection supported). The selected files are listed in the DICOM file list. The user can click any single DICOM file to read associated DICOM header and image preview. To manually create a matrix using DICOM files, choose files from the DICOM file list, press ‘>>>>>>’ to push the files into selected DICOM file list, provide a matrix name, press ‘Convert’ button to create a matrix based on chosen DICOM files. The user can load those created matrices into base workspace by pressing ‘Load matrix’ button.

Figure 6.4: MatrixUser DICOM File Loading Interface
Load DICOM file(s) in Batch
MatrixUser supports loading DICOM files in a batch mode. This function requires the path of the folder containing DICOM files is provided. MatrixUser will try to create separate matrices for DICOM files coming from different image series. A matrix selection interface will provide converted matrices with loading functions.
Load from NIfTI file
NIfTI file with .nii suffix is supported by MatrixUser.

6.2.2 Window Layout

To activate MatrixUser display window, press ‘MatrixUser’ button. If the selected matrix contains complex value, four options are available for displaying magnitude, phase, real and imaginary of the matrix. Figure 6.5 demonstrates an overview of the window layout of the MatrixUser display window. The window consists of

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Figure 6.5: MatrixUser Display Window

Matlab Default Toolbar

Matlab toolbar provides basic interactive functions for displaying matrix. These functions include:
- : Save current image axes into an image file
- : Zoom in matrix area
- : Zoom out matrix area
- : Manually move matrix position
- : Check individual voxel value and index
- : Print current figure
- : Turn on/off color bar
MatrixUser Function Library

Most of the matrix analysis functions are represented on function bench panel. MatrixUser groups these functions into categories and dynamically loads them according to the dimension size and compatibility of current display matrix. A multi-tab is used to contain individual function button associated with each function. The tabs under the multi-tab are used to switch between function categories, which include
- Display : Multi-dimensional matrix display functions
- QuickMath : Perform math calculation for current matrix
- Transform : Transform current matrix
- Process : Basic matrix processing functions
- ROI : Region-of-Interest functions
- Segment : Segmentation functions
- Surface : Generate surface or mesh plot for current image
- Matlab : Matlab default image tools
- More : Uncategorized functions
Matrix Calculator

The matrix calculator consists of three control items, including a matrix expression editbox, an execution button ( ) and a matrix saving button ( ). Valid matrix calculation expression can be executed in the calculator and updated in the display window, serving as a convenient way to analyze matrix calculation result. Matrix concatenation and recombination can also be done in the calculator, for example, to side-by-side compare multiple 3D matrices (Figure 6.6). Some valid calculation examples are, but not limited to:
- A,B Combines A and B in one row
- A,B;C,D Combines A and B in the first row, C and D in the second row
- A,B;C,zeros(size(C)) Combines A and B in the first row, C in the second row, pad with zero value
- sin(A),cos(B) Calculates voxel-wise sin for A and cos for B, then combine them in one row
- A(:,1:10,:) Extracts submatrix from A and display it
Figure 6.6: MatrixUser Concatenation Example

where A, B, C and D are multi-dimensional matrices with proper matrix size. Also note that the source matrices have to stay in the base workspace for being referenced. Pressing the execution button will perform the calculation and save the result as a temporary matrix. The user can also save the temporary matrix into workspace by pressing matrix saving button. The saved temporary matrix will have a ‘_tmp’ suffix by default.
Matrix Display Axes

The display axes renders an image for one slice of current matrix. The user can use mouse cursor to inspect the coordinate and value of any voxel. Moving mouse wheel back and forth moves the slice location along current dimension and updates the display axes.
Matrix Color Control Group

The matrix color control group provides a set of sliders, editboxes and popup menu which help control image color scheme and contrast. This group consists of
- Colormap Popup Menu: Choose different colormap scheme
- Upper Color Bound Slider (right slider): Slide to control the upper bound of color limits
- Upper Color Bound EditText (right editbox): Edit to control the upper bound of color limits
- Lower Color Bound Slider (left slider): Slide to control the lower bound of color limits
- Lower Color Bound EditText (left editbox): Edit to control the lower bound of color limits
Matrix Dimension Control Group

MatrixUser measures the dimension size of the display matrix and assigns one slider and editbox for each dimension that is above 2 (i.e. no slider and editbox for the first and second dimension). These control items are located in individual dimension tab and can be used to switch among slices in current active dimension.

6.2.3 Function Library

Display

Matrix display functions are listed under this tab.
- : Reset matrix display and erase additional display effect
- : Turn on and off black grid line on the image display axes
- : Open an instant magnifier which zooms in specific image area
- : Plot and update a profile curve along a resizable checking line (Figure 6.7)
  
  Figure 6.7: An Example of 1D Profile. The user can relocate and resize the profile checking line on the image for inspecting live 1D profile. The buttons on the profile window can list profile data, save the data as ‘data_plt’ array into workspace or copy the data into clipboard.
- : Plot and update a profile curve along a matrix dimension (Figure 6.8)
  
  Figure 6.8: An Example of Plotting the First (Column) and Second (Row) Matrix Dimension Profile. The user needs to specify which matrix dimension to plot. The profile curve will update according to current mouse cursor position. The user can pause or resume live updating by right click on main display window.
- : Open a separate window with two matrix display axes (Figure 6.9) displaying another two orthogonal images. The operation buttons on the second window consists of
  - : Activate or deactivate localizer line on main display
  - : Activate or deactivate localizer line on main display
  - : Switch matrices between main display and second display. This operation simply permutes current matrix into its orthogonal version. The user can save the transformed matrix using ( ).
  Figure 6.9: 3D Slicer. To change view slice, the user needs to activate localizer line and then click on desired coordinate on the main display window.
- : Create a RGB image, assign current slice and following two slices to Red, Green and Blue channel, respectively
- : Create a montage image using multiple slices (Figure 6.10)
  
  Figure 6.10: Montage Image. An example of creating a 4-by-5 montage image using multiple matrix slices starting from the first slice.
- : Overlap two matrices with the same matrix size (Figure 6.11), notice that the user can press to remove foreground matrix from overlapping with background matrix.
  
  Figure 6.11: An Example of Overlapping Two Matrices. A second window is provided for adjusting overlapping effect. The user can choose to overlap any size compatible matrices from the matrix list. There exist control items to change foreground colormap scheme, to modify image intensity fraction, or to change foreground color limits.
QuickMath

This function category performs quick math calculation for current matrix. A few commonly used math calculation are provided under this tab. Instead, complex calculation can be performed using matrix calculator as mentioned above.
- : Calculate absolute value
- : Calculate negative value
- : Calculate natural logarithm
- : Calculate base 10 logarithm
- : Calculate exponential
- : Calculate the power of 10
- : Calculate sine
- : Calculate cosine
- : Calculate tangent
- : Calculate inverse sine
- : Calculate inverse cosine
- : Calculate inverse tangent
Transform

This function category performs spatial transformation or fast Fourier transform (FFT) to current matrix.
- : Flip matrix horizontally (along the first dimension)
- : Flip matrix vertically (along the second dimension)
- : Flip matrix along slice direction (the third dimension)
- : Rotate matrix 90 degree in the counter clockwise direction
- : Rotate matrix 90 degree in the clockwise direction
- : Rotate matrix certain degree along an axis specified using the rotation axis origin and direction in the 3D space
- : Translate matrix along certain direction
- : Perform multi-dimensional FFT for current matrix, the user needs to specify up to which dimension to perform FFT.
Process

This function category performs basic matrix processing functions.
- : Create binary mask based on given threshold
- : Perform smoothing operation to current matrix
- : Perform sharpening operation to current matrix
- : Perform edge detection to current matrix
- : Provides various image filters (Figure 6.12)
  
  Figure 6.12: Image Filters. An example is shown for applying various image filters.
- : Add noise to matrix (Figure 6.13)
  
  Figure 6.13: Image Noise. An example is shown for applying various image noise.
- : Replace voxel value for the voxels within certain value range and outside a polygon area. The user needs to draw a polygon first (double click to confirm the polygon).
- : Replace voxel value for the voxels within certain value range and inside a polygon area. The user needs to draw a polygon first (double click to confirm the polygon).
- : Replace voxel value for the voxels inside a polygon area. The user needs to draw a polygon first (double click to confirm the polygon).
- : Replace matrix area with a selected matrix source region. The user needs to draw a free-hand area (source region), drag the free-hand region to target matrix area, then double click to confirm the operation.
- : Crop current matrix using a rectangle box (double click to confirm the cropping)
- : Extract parts of current matrix using irregular shape (double click to confirm the extracting)
- : Resample current matrix by using chosen interpolation method (Figure 6.14). The user can specify sampling factors in x, y and z direction for 3D matrix.
  
  Figure 6.14: Interpolation Window. An example is shown to double spatial resolution in x and y direction by using a linear interpolation.
ROI

MatrixUser provides a set of function buttons for performing Region-of-Interest (ROI) analysis (Figure 6.15). To create a ROI, the user needs to click ROI button first, then draw a ROI on the image axes. The statistical measures (i.e. mean, standard deviation and relative standard deviation) for voxels in delineated ROI is calculated and updated with moving ROI position or changing ROI shape. The ROI function buttons consists of
- : Draw a free hand ROI
- : Draw a rectangle or square ROI
- : Draw a circle or ellipse ROI
- : Draw a polygon ROI
- : Draw a straight line for measuring distance in units of pixels
- : Draw a polygon for measuring the interior angles in degrees
- : Record existing ROI shape and location into a ROI list, allow to redraw selected ROI in multiple image axes. To redraw a existing ROI, the user needs to select a ROI in the list, then press ‘Show’ button. Note that the copied ROI is no longer resizable and movable.
- : Plot histogram for current slice (Figure 6.16); if ROIs exist, plot histogram for latest activated ROI
Figure 6.15: Draw Multiple ROIs and Redraw on A Second Image. The source ROIs are in green, copied ROIs are in red.

Figure 6.16: Histogram for One Image Slice
Segment

MatrixUser supports functions for performing multi-slice manual segmentation. To create a segmentation, click segmentation button, then draw a region on the image axes. The user can modify the region location and shape prior to confirming segmentation with double click. The segmentation buttons consists of
- : Do a free-hand segmentation
- : Do a circle or ellipse segmentation
- : Do a polygon segmentation
- : Edit segmentation
- : Save segmentation into a MAT file
- : Load segmentation from a MAT file
Figure 6.17: Editing Segmentation

To edit segmented region (Figure 6.17), press to open a segmentation manager. The manager records the type and location for existing segmented regions. The user can click any region item to inspect the location of the region. To edit chosen region, click ‘Edit’ button to activate the region outline. Both the shape and mask flag are editable for segmented region. After editing, click ‘Update’ to conform modification. The user can press to save current segmentation into a MAT file which contains a mask matrix and a cell array storing segmentation location information. The user can also press to save the mask matrix into workspace. Pressing can load previous segmented regions from a saved MAT file. Notice that the user can press to remove segmentation from overlapping with background matrix.
Surface

This function category generates surface or mesh plot for current image.
- : Create contour plot of current matrix
- : Create 3D contour plot of current matrix
- : Create filled 2D contour plot
- : Create 3D shaded surface plot
- : Create surface plot and contour
- : Create surface plot with colormap based lighting
- : Create mesh plot
- : Create mesh plot and contour
- : Create a curtain around a mesh plot
- : Create a ribbon plot
- : Create a waterfall plot
- : Create pcolor (checkerboard) plot
Matlab

Matlab default image tools (Figure 6.18) are tailored for MatrixUser and included in this category.
- : Perform imtool for current image
- : Perform immovie for playback current 3D matrix
- : Perform imcontrast for adjusting image contrast
Figure 6.18: Matlab Tools
More

Uncategorized functions are categorized under this tab.
- : Create a 3D graph for rendering current matrix (Figure 6.19)
  
  Figure 6.19: An Example of 3D Human Brain Rendering. Control units on the rendering window are provided for fine tuning the renderer. The user can select isosurface threshold, cutoff connectivity threshold (i.e. object with total voxels less than the threshold will be removed from the rendering. ‘@’ is followed by the voxel number of current largest object) and object opacity. A set of pushbuttons are also available for changing surface color, display box and patches. The default Matlab camera toolbar are provided for adjusting the lighting effect.
- : Perform projection along a given matrix dimension. Support multi-dimensional matrix projection
- : Perform 3D projection along x, y or z axis with certain angle increment (Figure 6.20)
  
  Figure 6.20: 3D Maximum Intensity Projection (MIP). An example of 3D MIP around axial axis of a human knee MRI image stack shows the vascular system of the knee joint.
- : Reslice 3D matrix at given direction. The user needs to draw a line for indicating the slicing direction with double click for confirmation (Figure 6.21)
- : Create a movie using current matrix display. Support making movie for overlapped matrices.
Figure 6.21: Reslice 3D Matrix. An example of 3D reslicing generates a new stack of images in the oblique plane from an axial human knee MRI image stack. Note that the resliced images are extracted from the plane perpendicular to the indicating line on the left window.

6.3 arrayShow

The arrayShow tool is a Matlab image viewer which has been designed for the evaluation of multidimensional complex images. arrayShow is originally designed by Tilman Johannes Sumpf at Biomedizinische NMR Forschungs GmbH. The user can press ‘arrayShow’ button to activate this viewer. Detailed information about arrayShow can be found at http://www.biomednmr.mpg.de/index.php?option=com_content&task=view&id=137&Itemid=43;

6.4 SpinWatcher

The SpinWatcher is designed for monitoring spin evolution behavior within a single voxel at given MR sequence and field environment. This function can be activated by pressing ‘SpinWatcher’ toolbar icon located at the top of the main simulation console.

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Figure 6.22: SpinWatcher Toolbar Icon

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Figure 6.23: SpinWatcher Main Interface

Figure 6.23 demonstrates an overview of the SpinWatcher main interface. This interface consists of

Voxel Locator
The default voxel is chosen as the one at the isocenter indicated by a red isocenter marker. However, the user can select any voxel within the virtual object by using . The slider beside the image can help change image slices.
Spin Property and Environment

The spin properties will be automatically updated with a selected voxel. The user can modify the spin properties and environment to meet their own needs. The editable properties provided in this interface include:
1. Spin
  - ChemShift (Hz/T): The chemical shift of the spin
  - Gyro (rad/s/T): The gyromagnetic ratio of the spin
  - Rho : The density of the spin
  - T1 (s): The longitudinal relaxation time
  - T2 (s): The transverse relaxation time
  - T2Star (s): The T2* relaxation time
  - SpinPerVoxel : The number of spins in each voxel, default one spin per voxel will treat T2* equal to T2, use a number above one for simulating T2* effect
  - TypeNum : The number of spin species
  - LocZ : The Z location of the selected voxel
  - LocY : The Y location of the selected voxel
  - LocX : The X location of the selected voxel
2. Display
  - WindowSize : The window width of the spin evolution plot
  - ISOHighlight : The flag for turning on and off isocenter mark
  - Grid : The flag for turning on and off grid line
  - Axes : The flag for turning on and off axes label
The SpinWatcher supports monitoring multiple spin species. The user needs to provide an array of multiple values for T1, T2, T2*, Rho and ChemShift, and give the correct number of spin species. The values must be separated with space. For example
- ChemShift = 0 -210
- Rho = 1.0 0.5
- T1 = 1.2 1.0
- T2 = 0.02 0.03
- T2Star = 0.002 0.003
- TypeNum = 2
Spin Watcher Window
A 3D spin evolution animation is displayed in the spin watcher window. The 3D animation is controllable using a set of control buttons and sliders
- Scroll Bar : Drag the scroll bar to any intermediate time point between beginning and end
- | < : Move to the beginning
- X : Pause animation, notice that the interface can only be closed while animation is paused
- O : Resume animation
- > : Play at normal speed
- >> : Play at double normal speed
- > | : Move to the end
Spin Evolution Plot

SpinWatcher provides two plots for capturing the spin evolution (i.e. |Mxy| and Mz) regarding time. Press ‘Execute’ button to recalculate the spin evolution plot if changes to spin property and environment was made. The settings can be saved into a file by pressing ‘Update’. To export temporary variables of spin evolution into Matlab base workspace, press ‘Export’, the exported variables include :
- Muts : A array for time points
- MxySum : A array for |Mxy|
- MzSum : A array for Mz
- Mx : x component of magnetization
- My : y component of magnetization
- Mz : z component of magnetization
The user can also undock the spin evolution plot by pressing ‘∧’ button.

6.5 SARWatcher

The SARWatcher is a graphical toolbox for monitoring time varying spatial Specific Absorption Rate (SAR) of the virtual object under given experimental design. This function can be activated by pressing ‘SARWatcher’ toolbar icon located at the top of the main simulation console. Note that in order to evaluate SAR, transmitting RF coil with E1 field is required. One example can be found at Coil_8ChHeadSAR.

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Figure 6.24: SARWatcher Toolbar Icon

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Figure 6.25: SARWatcher Main Interface

Figure 6.25 demonstrates an overview of the SARWatcher main interface. This interface consists of

SAR/Power
The SAR/Power panel displays time varying spatial SAR and power map for the virtual object. The user can choose different time point (horizontal scroll bar) and slice (vertical scroll bar) to inspect map details.
Local SAR Settings
The ‘Spatial’ and ‘Temporal’ tab on the ‘Local SAR Settings’ panel contain parameters for controlling SAR and power calculation.
1. Spatial
  - N_Gram (g): The number to specify averaged N-gram SAR, set to 0 indicating unaveraged spatial SAR
2. Temporal
  - tStart (s): The starting time to calculate SAR
  - tEnd (s): The ending time for SAR calculation
  - dt (s): The nominal time interval for SAR calculation
  - N_Second (s): The nominal time window for SAR calculation
Time Point Table
The Time Point Table contains a list of time point (s) and N_Second (s) in actual SAR calculation, this is because SAR calculation only updates at execution points.
SAR Stats
The SAR Stats panel contains overall statistics for calculated SAR and power at given time point.

The user can export the SAR and power map in a separate window by pressing ‘Export’ button. Pressing ‘Update’ button updates any modifications. The spatial SAR and power calculation follows the methods described in literature [11, 12]. The spatial N-gram SAR averaging is implemented using a method described in literature [13].

6.6 SeqConverter

(:TODO) SeqConverter is a graphical toolbox for converting MRiLab MR sequence format to more portable sequence format. This toolbox is still under developing.

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Chapter 6Image Display and Analysis

6.1 MagicRightClick

6.2 MatrixUser

6.2.1 Data Import

6.2.2 Window Layout

6.2.3 Function Library

6.3 arrayShow

6.4 SpinWatcher

6.5 SARWatcher

6.6 SeqConverter

Chapter 6
Image Display and Analysis