DENSEms manual - DENSEanalysis

DENSEms manual - DENSEanalysis
DENSEms
Multi-slice module for the DENSEanalysis software
Software release 2011a
2011.06
User Manual
Andrew D. Gilliam, Ph.D.
image & video analysis • consulting engineer
NOTE FROM THE CREATOR…
Welcome to the DENSEms tool! With this software, you can:
• Simultaneously access multiple slices of short-axis left-ventricular DENSE displacement data
• View multi-slice left-ventricular motion
• Quantify multi-slice twist and torsion
SYSTEM REQUIREMENTS
•
•
•
•
Matlab
Matlab Image Analysis Toolbox
Matlab Spline Toolbox
Matlab C-compiler
This tool has been tested using 64-bit Windows 7 and 64-bit MATLAB r2010. Other operating systems
and newer MATLAB versions will probably still work, but no guarantees.
We assume users have knowledge of MATLAB as well as the look and feel of the acquired data. This
document is not a primer on MATLAB or the acquisition system!
We also assume users are already familiar with the main DENSEanalysis software package. Please see
the DENSEanalysis manual for more information.
1
TABLE OF CONTENTS
1. Installation & Startup ................................................................................................................................ 3
1.1. Prior to installation .......................................................................................................................... 3
1.2. Installation ....................................................................................................................................... 3
1.3. Startup ............................................................................................................................................. 3
2. DENSE Analyses ......................................................................................................................................... 4
3. Interface .................................................................................................................................................... 5
4. Files ........................................................................................................................................................... 6
4.1. Load Files ......................................................................................................................................... 6
4.2. Unload Files ..................................................................................................................................... 7
5. Display ....................................................................................................................................................... 8
5.1. Plot Selection ................................................................................................................................... 8
5.2. Slice Selection ................................................................................................................................ 10
5.3. Base/Apex Slice Order ................................................................................................................... 11
5.4. Slice Names & Colors ..................................................................................................................... 12
5.5. Alternative 3D Coloring ................................................................................................................. 13
5.6. 3D View.......................................................................................................................................... 14
5.7. Regional Twist Options .................................................................................................................. 14
5.8. Background/Axes/Text Color......................................................................................................... 17
5.9. Playbar ........................................................................................................................................... 17
5.10. Twist/Torsion Range .................................................................................................................... 15
5.11. Twist Colormap............................................................................................................................ 16
6. Export ...................................................................................................................................................... 18
DENSEMS: TABLE OF CONTENTS
2
1. INSTALLATION & STARTUP
The DENSEms module is included with the latest version of the DENSEanalysis software. Simply unzip
the DENSEanalysis.zip file to install.
1.1. PRIOR TO INSTALLATION
• Ensure you meet the aforementioned system requirements
• If you have never compiled a mex-file in MATLAB before, run
mex-setup in the MATLAB command window to select a
compiler on your machine.
On 32-bit Microsoft Windows platforms, MATLAB provides a C
compiler. Alternatively, look here:
http://www.mathworks.com/matlabcentral/fileexchange/22689
• If you have a previous installation of the DENSEanalysis software,
remove any existing search paths pointing to that installation and
restart MATLAB (from the MATLAB File Menu, choose Set
Path and remove folders referring to the previous installation).
1.2. INSTALLATION
• Unzip the DENSEanalysis.zip file to a location of your choice
• Open MATLAB
• Navigate MATLAB to the new DENSEanalysis folder
• Run DENSEsetup in the MATLAB command window
If DENSEsetup failed for any reason, the DENSEanalysis program will not function as expected!
1.3. STARTUP
• Open MATLAB
• Navigate MATLAB to the new DENSEanalysis folder
• Run DENSEms from the MATLAB command prompt
DENSEMS: INSTALLATION & STARTUP
3
2. DENSE ANALYSES
Before we may access and evaluate multiple slices of short-axis left-ventricular DENSE data via the
DENSEms utility, we must first recover tissue displacement from each individual slice via the
DENSEanalysis tool. This section outlines a typical DENSEanalysis workflow; please refer to the
DENSEanalysis manual for more information.
• Run DENSEanalysis from the Matlab command line
• Create a new patient workspace or access
an existing patient workspace with one or
more short-axis slices of DENSE data.
• For each short-axis DENSE slice, define a short-axis region of interest
delineating cardiac anatomy.
• Select Run Analysis from the Analysis menu to estimate tissue
displacement from the DENSE data.
• Explore the completed analysis to ensure accurate phase
unwrapping and plausible displacement measurements.
• Access the cardiac model tool by exploring any strain visualization
option or by selecting Cardiac Model within the analysis tab.
• Define short-axis cardiac parameters, ensuring an appropriate
cardiac model for the given slice (typically a four-element model for
apical data and a six-element model for mid-ventricular and basal
data).
• Select Export MAT from the Export menu to export a Matlab
compatible file containing the completed analysis.
• Repeat the analysis process for all parallel cardiac short-axis slices
from a given study/patient.
• We suggest you gather all analysis files (.mat) in a single folder for
easy bookkeeping.
DENSEMS: DENSE ANALYSES
4
3. INTERFACE
Below is a snapshot of the DENSEms tool. For specific information on each available option, refer to the
appropriate section of this manual.
Menu & Toolbar
Load/unload analysis files,
export images & videos, etc.
Plot Selection Tool
Select slice & main panel display
Main Window
Navigate
multi-slice analyses
Display Tool
Main panel display options
DENSEMS: INTERFACE
5
4. FILES
To begin multi-slice analysis, we must load multiple short-axis analysis files exported from the
DENSEanalysis tool into the DENSEms utility.
IMPORTANT NOTES REGARDING ANALYSIS FILES
• Analysis files must be generated using the latest version of the DENSEanalysis software.
Previous exports are not compatible with the DENSEms utility.
• Files must be derived from a single study/patient
(i.e. all image information must have the same StudyInstanceUID).
• All regions of interest must delineate short-axis left-ventricular cardiac anatomy.
• Slice planes must be unique and parallel.
• Frame indices are assumed to be perfectly aligned (i.e. we assume frame 1 was acquired at the same
cardiac phase for all slices, as was frame 2, frame 3, etc.).
4.1. LOAD FILES
• Select Load File(s) from the File menu.
• Navigate to the appropriate directory and select one or
more analysis export files generated using the
DENSEanalysis software.
• Select Open.
• View the file load report.
− Failure to meet the file criteria above (DENSEanalysis
export files, single study, short-axis cardiac anatomy,
unique and parallel slices) will result in a load failure.
DENSEMS: FILES
6
4.2. UNLOAD FILES
• Select Clear File(s) from the File menu.
• Select files to remove.
• Select OK.
DENSEMS: FILES
7
5. DISPLAY
Users have access to several multi-slice displays,
accessible through the Plot Selection tool,
including:
• 3D material point displacement
• Twist and torsion versus time
• Regional twist
Users may change the appearance of each display
via the Display Options tool.
5.1. PLOT SELECTION
Access different displays through the Plot Selection buttons.
3D Displacement
This option allows users to navigate material point locations for all
loaded slices for any frame of interest.
In addition to material point locations represented by small circles,
the software displays the epicardial centroid as a small square.
DENSEMS: DISPLAY
8
Twist/Torsion vs. time
This option accesses average twist per slice as a function of time,
and torsion as a function of time.
Twist quantifies material point rotation around the left ventricular
centerline, measured in degrees.
− Material point rotation is measured with respect to the
epicardial centroid of each slice for each frame.
− Positive twist is defined as a counter-clockwise material point
rotation when viewed from the apex of the left ventricle (the
traditional MR view).
Average Twist quantifies the average twist per slice among all
material points for each frame, measured in degrees.
Torsion quantifies the change in average twist per unit longitudinal
length, measured in degrees per mm of length.
− For each neighboring slice pair, we quantify the change in
average twist over the distance between slices. We average
these values to produce our torsion measurement.
− Positive torsion indicates a decrease in average twist from
apex to base.
Regional Twist
This option allows users to visualize average twist values within
radial segments of cardiac anatomy.
Regional Twist measures the average twist in a specific radial
segment of cardiac anatomy, measured in degrees.
The displayed layers traverse slices of cardiac anatomy from the
basal level in the outer layer to the apical level in the inner layer.
Slices are colored according to the twist range (Section 5.8) and
twist colormap (Section 5.9).
Radial segments are displayed according to the standard American
Heart Association model, as viewed from the apex of the left
ventricle. The anterior, septal, inferior, and lateral directions are at
12, 9, 6, and 3 o’clock, respectively.
DENSEMS: DISPLAY
9
5.2. SLICE SELECTION
Select a slice of interest via the Slice Selection dropdown box.
This slice will be highlighted in each plot, as displayed below.
No slice Selected
No slice Selected
Selected
Slice
Slice Selected
Slice Selected
Selected
Slice
DENSEMS: DISPLAY
Selected
Slice
10
5.3. BASE/APEX SLICE ORDER
The software has predefined basal and apical directions, enabling the regional twist display to place the
apical-most slice on the inner-most level of the display. Users may reverse the slice order should the
basal and apical slices not lie in the expected direction.
• Select the 3D displacement display option.
• Compare the Base/Apex Orientation axes to the 3D
Displacement display.
• Should the basal and apical slices not lay in the
expected and labeled directions, select
Reverse Base/Apex Slice Order.
DENSEMS: DISPLAY
11
5.4. SLICE NAMES & COLORS
The name and color of each slice are important identifiers:
− In the 3D Displacement display, material points can be colored according to the slice color.
− In the Twist/Torsion vs. Time display, lines are colored and labeled according to the
respective slice color and name.
• Select a slice of interest.
• Right-click the Slice Selection dropdown box.
• Select from the available options.
Rename Slice
• Modify the slice name.
• Select OK.
Recolor Slice
• Modify the slice color.
• Select OK.
DENSEMS: DISPLAY
12
5.5. ALTERNATIVE 3D COLORING
Users may select from alternative 3D material point color schemes, coloring points according to their
radial segment or twist value rather than the slice color.
Radial Segment Coloring
• Select the 3D displacement display option.
• Select the Segment option from the 3D
coloring dropdown menu.
• Compare the Radial Color Sample axes to the
3D Displacement display to locate each radial
segment.
− As the radial color sample is viewed from
the apex, we suggest viewing the 3D display
from the apex.
Twist Coloring
• Select the 3D displacement display
option.
• Select the Twist option from the 3D
coloring dropdown menu.
• Each material point in the
3D Displacement display is colored by its
twist value, according to the twist range
(Section 5.8) and twist colormap
(Section 5.9).
DENSEMS: DISPLAY
13
5.6. 3D VIEW OPTIONS
• Select the 3D Displacement display.
• Left-click, hold, and drag within the 3D box to
rotate the 3D view
• Right-click within the 3D box to select from
available views.
5.7. REGIONAL TWIST OPTIONS
• Select the Regional Twist display.
• Right click any regional twist layer.
• Select from the available options:
− Toggle text for all layers on and off
via the Display Text option
− Adjust the number of segments in
the selected layer.
DENSEMS: DISPLAY
14
5.8. TWIST/TORSION RANGE
• Enter new range values to adjust the twist and torsion ranges within the
Twist/Torsion vs. Time and Regional Twist displays.
Twist/Torsion vs. Time
Regional Twist
Twist
Range
Twist
Range
Torsion
Range
DENSEMS: DISPLAY
15
5.9. TWIST COLORMAP
Select Colormap
• Select a colormap from the Twist Colormap dropdown menu.
Jet
Copper
High/Low (Grayscale)
New Colormap
• Right click the Twist Colormap dropdown menu.
• Select New Colormap.
• Enter a name for your colormap.
• Enter a matlab command for your colormap.
− The matlab command must evaluate to an [Nx3] matrix, where N
is between 1 and 128. The colormap spans the minimum to the
maximum of the twist range.
• Select OK.
Delete Colormap
• Right-click the Twist Colormap dropdown menu.
• Select Delete Colormap.
• Select OK.
DENSEMS: DISPLAY
16
5.10. BACKGROUND/AXES/TEXT COLOR
• Select a color option:
− Background Color
− Axes Color
− Regional Twist Text Color
• Modify the color.
• Select OK.
5.11. PLAYBAR
• Navigate through time via the playbar:
− Scroll through the frames
− Enter a specific frame of interest
− Play all frames in a continuous loop.
DENSEMS: DISPLAY
17
6. EXPORT
Users may export high-resolution images and videos of the main display window, suitable for inclusion
in papers and presentations. Users may also export twist & torsion measurements to a data file.
Image/Video export
Images and videos are captured directly from the current display. Videos traverse all available frames.
Users may select from a number of image and video formats, including:
− Bitmap image (*.bmp)
− Portable Network Graphics image (*.png)
− Enhanced Metafile (*.emf)
− TIFF image (*.tiff)
− EPS file (*.eps)
− Uncompressed TIFF image (*.tiff)
− JPEG image (*.jpg)
− AVI file (*.avi)
− Portable Document Format (*.pdf)
− Animated GIF file (*.gif)
• Select Export Image/Video from the File menu
− Navigate to the appropriate directory
− Enter the file name to be exported
− Select the appropriate file type
• Select OK.
• Select from the available export options
− Size
Select the screen size, or enter the height & width in inches
− Resolution
Select the screen resolution, or enter resolution in dpi
− Video speed:
Frames Per Second (for AVI/GIF only)
− Compression
AVI compression (for AVI only)
• Select OK.
Measurement Export
Users can output a comma delimited text file (csv) or a Microsoft Excel spreadsheet (.xls) of the average
twist, torsion, and regional twist values per frame.
• Select Export Measurements from the File menu
− Navigate to the appropriate directory
− Enter the file name to be exported
− Select the appropriate file type
• Select OK.
DENSEMS: EXPORT
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