Checkpoint Manual

User Manual
February 23, 2017
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Copyright 2005 - 2017 by Stratovan Corporation. All rights reserved.
Table of Contents
Contents
Purpose ......................................................................................................................................................... 4
Login Screen .................................................................................................................................................. 4
Internet Updates ........................................................................................................................................... 6
Specimen Tab ................................................................................................................................................ 6
Image Stacks ................................................................................................................................................. 8
Image Viewing Layout ................................................................................................................................. 11
Volume Tab ................................................................................................................................................. 14
Surface Tab ................................................................................................................................................. 15
Toolbar Icons............................................................................................................................................... 17
Landmark Primitives ................................................................................................................................... 20
Combining and Splitting Landmark Points .................................................................................................. 27
Landmarks Tab ............................................................................................................................................ 29
Template Tab .............................................................................................................................................. 37
Landmarks Not on a Surface ....................................................................................................................... 45
Export Tab ................................................................................................................................................... 46
Export Volumes ........................................................................................................................................... 47
Export Surfaces ........................................................................................................................................... 48
Export Landmarks ....................................................................................................................................... 49
Export Cropped Volumes and Surfaces....................................................................................................... 50
Shape Analysis Tab ...................................................................................................................................... 52
Stratifications .............................................................................................................................................. 54
Shape Analysis: Average ............................................................................................................................. 56
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Shape Analysis: Generalized Procrustes Analysis ....................................................................................... 58
Shape Analysis: Joint Congruence............................................................................................................... 59
Warping Tab ................................................................................................................................................ 64
Tutorial A: Joint Congruence Using a Joint Primitive ................................................................................. 71
Tutorial B: Joint Congruence with Two Patches ........................................................................................ 76
Checkpoint File (*.ckpt) .............................................................................................................................. 81
Customer Support ....................................................................................................................................... 82
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Purpose
Stratovan CheckpointTM enables you to collect thousands of landmark and semi-landmark points in 3D.
Checkpoint can import both surface meshes and volumetric DICOM scans, and extract multiple surfaces
from a DICOM volume. Our easy-to-use landmark editing interface allows you to quickly place single
points, curves, and patches in order to represent the morphology of your specimen. The landmark and
semi-landmark points can then be exported to use with popular shape analysis software tools, or your
own custom processing software.
Login Screen
On a computer with Internet access and Checkpoint installed, login by entering your account email and
password, then click Submit. This is the same account information you use to log into our website:
http://www.stratovan.com/user/login
You can obtain a username/password by signing up for a free trial or by purchasing the software.
Figure 1: Checkpoint login screen
Begin a free trial by clicking on Signup Now! which will ask you to fill in information to create an
account.
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Figure 2: Start a free trial by creating an account
If an Internet connection is unavailable for the computer with Checkpoint installed, enter your login
email, then click on Node Lock. A window, shown below in Figure 3, will pop up. Click on Copy to
Clipboard and paste the information in an email to support@stratovan.com. When you receive an
email from us with your code then start Checkpoint, enter your login email, click on Node Lock, enter
the code, and click on Lock. When Checkpoint starts up, enter your login email address, then click
Submit. To remove the node lock, click on Node Lock at the login screen, then click on Unlock.
Figure 3: Set up node lock to avoid Internet-based login
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Internet Updates
You will be notified, after logging in, if a newer version of our software is available. You can also select
Help | Check for Updates to check for and download the latest application updates, if any are available.
If you are using a node locked license, then you will need to download and apply the update. Log into
your account and go to https://www.stratovan.com/user/applications. The update will invalidate the
node lock, so you need to click on Node Lock on Checkpoints login screen, copy the information
provided and send it in an email to customer support.
Specimen Tab
The specimen tab, seen below in Figure 4, allows you to load specimen data files. Click the Browse
button to select a folder, and Checkpoint will scan all sub folders for specimen data. Select a file from
the list in the panel marked Specimen List, then click the Open button to load the file. See the
Image Stacks section below for instructions on loading a series of images.
Figure 4: Specimen tab shows a list of specimen files and allows you to open the specimen file selected
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Table 1 below lists the supported formats for importing and exporting data.
Import Export
Volume Surface Landmarks Surface Volume
DICOM PLY CSV PLY NifTI
TIFF/JPG Image OBJ Morphologika OBJ FITS

Stack
STL NTSYSpc STL
ANALYZE
WRL IDAV Landmark
NifTI Editor
FITS
Table 1: Supported import and export formats. If you need a certain file format, please email
support@stratovan.com to request it.
Enter a file name into the Search box to find a specific file within the specimen list, or use partial file
names as a way to filter out other files. In Figure 5 below, a list containing files Series_a_1,
Series_a_2, Series_b_1, and Series_b_2 can use a search of series_a to filter the list to only
show Series_a_1 and Series_a_2. The search value can also use a file name such as _1 to filter the
list to only show Series_a_1 and Series_b_1.
Figure 5: Using Search to filter the specimen list. The left image shows the full specimen list. The middle image
shows the list filtered with series_a. The right image shows list filtered with _1.
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Image Stacks
Checkpoint can load an image stack represented by either a series of TIFF or JPG files, or a single TIFF file
containing several images. In the specimen tab, click Image Stack to bring up the dialog box below in
Figure 6.
Figure 6: Select image files to use, provide a name and spacing, then save the configuration
Click Select Image Files and select all the image files. The selected files will appear in a list under 2.
Order Image Files. To replace a list, click Select Image Files again and select the new image files. The
list is alphabetical by default, but allows you to change the order by clicking on a file in the list and then
clicking Move Up or Move Down as seen in Figure 7 below. Clicking the Reverse button reverses
the order of all of the image files.
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Figure 7: Manually sort images, if needed, with "Move Up" and "Move Down" buttons
Under Stack Properties, enter a name for the image stack as well as the spacing and units. Under
Save Stack Information, select an output format from the combo box, like .ckpt, and click Save
Stack. This creates a file in the same directory as the image files, which Checkpoint can then use to
load the image stack with the proper spacing and units. A pop up box indicates the full path to the file.
With the new file created, click Browse in the specimen tab and select the folder that contains the
image stack.
For example, in Figure 8 below, a file called MyImageStack.ckpt is created in the same folder that
holds the TIFF files listed under 2. Order Image Files. Figure 9 below shows the specimen tab browsed
to C:\tmp, which contains all the TIFF files used and MyImageStack.ckpt, which appears in the
specimen list and can be loaded by selecting it and clicking Open.
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Figure 8: Creates an image stack file called "MyImageStack.ckpt"
Figure 9: Load in the image stack with "MyImageStack.ckpt"
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Image Viewing Layout
The window labeled 3D shows volumetric or surface data. The slice windows, labeled Axial,
Coronal, and Sagittal show a single 2D slice through the 3D data. The sliders change the viewed
slice. Clicking on a small panes name button will bring that window to the large pane. For example, in
Figure 10, clicking on Axial will move the axial window into the large pane and move 3D window into
the small pane.
The text found at the bottom of the large pane, detailed in Figure 11, provides scan and application
information such as volume dimensions, volume spacing, triangle count in the surface mesh, the
application version, video RAM used and rendered frames per second.
Figure 10: Layout overview. Three slice windows are along the left-hand side. A 3D view is shown in the middle
with a data intensity histogram shown along the right-hand side (if the specimen is volumetric data).
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Figure 11: Detailed scan information
Zoom In/Out of Slice Window: Hold CTRL and use the mouse wheel.
Zoom In/Out of 3D Window: Use the mouse wheel or hold CTRL and left-drag the mouse left-and-right
or up-and-down in the window to zoom.
Reset Window: Right click in any window and select Reset [window] View where [window] is the
name of the window (i.e. The Axial window will show Reset Axial View). The reset options also reside
in View | Reset menu.
Move Slices: Right click and drag in a slice window.
Move to Next/Previous Slice: Use the mouse wheel in a slice window or drag a slider, as depicted
above in Figure 10, or drag a slice avatar bar in a slice window, as seen below in Figure 12, with a left
click, or drag the slice avatar in a slice window, as seen below in Figure 14, by left clicking.
Rotate Slices: Drag a slice rotation handle with a left click in the slice window, as illustrated below in
Figure 13.
Move 3D Volumes/Surfaces: Right click and drag in the 3D window.
Rotate 3D Volumes/Surfaces: Left click and drag in the 3D window. Middle mouse (mouse wheel
button) click and drag in the 3D window to rotate around the viewing axis.
Screen Shot: Right click a window and select Capture | Capture Image.
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Figure 12: Slice avatar bars. Drag to change the Figure 13: Slice rotation handles. Drag to rotate
slice position. the slice.
Figure 14: Slice avatar center. Drag to change the slicing position.
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Change Displayed Units: Select new units in View | Display Units. These units appear in the
datas bounding box in the 3D window, as seen below in Figure 15.
Figure 15: Display units. The top-image shows mm and the bottom image shows m. Please see note
below.
Surface data files such as PLY, STL, OBJ, and WRL do not retain unit information for the point
coordinate. (DICOM scans, for example, are always stored in mm.) This can result in confusing
unit displays in Checkpoint since it has to guess what the units are stored in the file. You can
change the specimen file units explicitly from the menu with View | Specimen Units (per the
file). However, software such as Geomagic sometimes changes the units of a surface without
approval by, or the knowledge of, the user.
Volume Tab
The volume tab, exhibited below in Figure 16, presents the DICOM volumetric data in the 3D
window and in the three slice windows. This tab is only used when the loaded specimen scan
has volumetric data.
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Figure 16: Volume tab. The data intensity histogram is shown along the right-hand side of the 3D window.
You can change the contrast and brightness of the scan by left-clicking and dragging it in the
slice windows up-and-down and left-and-right.
Volumetric rendering is dependent on your computer's video hardware. We recommend using

medium- to high-quality video hardware from nVidia or AMD/ATI to achieve the best
performance. Low quality video hardware will render this view slowly, less than five frames per
second (FPS), and in some cases may not render it at all or crash the software. Upgrading your
computer system to a higher-quality video card will often resolve this issue. Send an email to
support@stratovan.com for hardware recommendations.
Surface Tab
The surface tab, depicted below in Figure 17, presents the loaded or extracted surface mesh in
the 3D window. The slice windows show the intersections with the surface mesh and the 2D
volume slice, seen below in Figure 18.
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Figure 17: Surface tab.
Figure 18: The left image shows a slice through the volume. The right image shows the volume slice and
surface intersection (shown in red).
The data histogram, on the right side of the 3D window (detailed below in Figure 19), can
change the iso value used for isosurfacing. Hold CTRL and left-click on the histogram to set a
new iso value and recompute the isosurface. Alternatively, right-click on the histogram and
select Add a New Isosurface. This brings up a pop up box that allows an exact iso value to be
set, as well as a checkbox that will set the new iso value as the default for scans of the same
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modality (e.g., a default for a CT scan will not be used for an MRI scan). If a default value is set,
then it will be used on all future scans loaded that share the same modality. Iso values may only
be created when the surface mesh is visible. Red indicates the current iso value, while blue
indicates saved iso values, which can restore themselves by left-clicking on the line below the
number. For example, in Figure 19, to restore iso value 563, hover the mouse over the blue line
below 563, which should then change color from blue to yellow, and left-click.
The current iso value may be deleted by left-clicking the red X on the right side of the number
in parenthesis, as seen in Figure 19. This deletion option only appears when more than one iso
value exists. Alternatively, right-click on the histogram and hover over Delete Iso Value, then
select the iso value to delete it from the sub menu.
Figure 19: Data histogram with four extracted isosurfaces (1175, 563, 200, and -290). The currently
selected and rendered isosurface is indicated in red.
Toolbar Icons
Landmark Primitive Icons
: Click to enable adding single points. Hold shift, then left-click to add a single point.
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: Click to enable adding curves. Hold shift, then left-click to add points to the curve. To
append points to an existing curve, select an end point on the curve then hold shift and left-
click to add a new point.
: Click to enable adding patches. Hold shift, then left-click to add patch.
: Click to enable adding joints. Hold shift, then left-click to add a joint.
: Click to enable editing landmark. This mode enables adding length, angle and plane
primitives. Selected landmarks are colored red, white, blue and green.
Landmark Measurement Icons
: Select two landmarks then click on this icon to create a length primitive between the two
landmarks.
: Select three or four landmarks, then click on this icon to create an angle primitive. Angles
are defined by red, white and blue for three points or red, white, blue and green for four points.
: Select three or four landmarks, then click on this icon to create a plane primitive. Planes
with four points are positioned at the average of the points.
Landmark Joining Icons
: Select two landmarks, red and white, then click on this icon to combine them to the red
landmarks position.
: Select a landmark thats been combined with other landmarks, then click on this icon to
split it up again. Split landmarks are positioned in the normal vectors direction.
: Unpins the selected patch point, allowing it to automatically reposition when patch
control points move.
View Option Icons
: Enable or disable lighting for volumetric data. Disable to improve performance.
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: Show or hide volumetric data.
: Show or hide the surface mesh.
: Show or hide cropping lines.
: Enable or disable a 3D cut-away at the avatars position
: Decrease the size of landmarks and semi-landmarks.
: Increase the size of landmarks and semi-landmarks.
: Set the surface meshs opacity. Set to 100% to improve performance.
: Show or hide landmark points.
: Show or hide semi-landmark points; also toggles rendering of curve lines and patch lines.
: Show or hide semi-landmark labels.
: Show or hide directions of curves and patches.
: Show or hide the bounding box.
: Change background color to white or black.
User Interface Font Icons
: Increase applications font size.
: Decrease applications font size.
: Set application font size to default.
: Info about Stratovan Relay TM.
Data Icons
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: Save your landmark data.
: Undo/redo the most recent operation.
Landmark Primitives
Primitives can be added in the 3D window on the surface mesh as well as in a slice window.
Each primitive may be given a name and marked as missing. Primitive overlays, seen below in
Figure 20, appear in the large pane in the volume tab and the surface tab. Right-click on the
overlay to set the primitives name, toggle the missing flag or delete the primitive. Curves,
patches, and joint primitives have the added option Crop to Primitive, which will move the
crop bounds closely around the primitive. The landmark tab holds these options as well as
several other primitive editing options.
Figure 20: Primitive overlays always appear in the large pane. You can select landmark points and other
primitives easily from these icons.
Select Landmarks: Left-click a landmark to select it.
Select Primitives: Select a landmark on the primitive or left-click on a primitives overlay in the
surface tab or the volume tab, or left -lick a primitive in the landmark tab.
Unselect Landmarks/Primitives: Left-click in a slice window, or the 3D window, then press the
spacebar.
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Delete Primitives: Select a landmark on the primitive and press delete on the keyboard, or
right click on a primitives overlay, located on the left side in the large pane, and select Delete
Primitive from the popup menu.
Single Points: A single point consists of a single landmark. Click the icon, then hold shift
and left-click to add a single point. Figure 21 depicts a single point. The arrow represents the
normal of the surface.
Figure 21: Single point with normal vector
Curves: Curves consist of two or more landmark control points and automatically generate
semi-landmark in between. Click the icon, then hold shift and left-click to add a landmark
to the curve. Each curve can have landmarks appended. Figure 22 illustrates the curve creation
process. The curves direction and semi-landmark density can be changed in the landmark's tab,
as seen in Figure 37 in the landmark's tab section. Semi-landmarks can be marked as missing in
the landmark tab. Figure 23 shows a curve with direction.
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Figure 22: Curve created with four landmarks. Landmarks are added from A to D.
Figure 23: Curve direction indicated by arrows.
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Patches: A patch consists of a landmark grid, of which the border landmarks and the center
landmark are selectable and moveable. Click the icon, then hold 'shift' and left-click to add a
patch. The patchs direction and semi-landmark densities can be changed in the landmark tab
(see Figure 40) in the landmark's tab section. Semi-landmarks can be marked as missing in the
landmark tab. Patch orientation, seen in Figure 24, is either clockwise or counter-clockwise.
The blue circle in the corner indicates that the landmark in that corner shall be the first exported
landmark during the patchs exporting process.
Figure 24: Patch orientation indicated by circular swoosh
Joints: A joint consists of two point-matched patches, one on each opposing surface (e.g., the
condyle and the fossa for temporomandibular joint (TMJ). Click the icon, then hold 'Shift'
and left-click to add a joint. The condyle patch renders with blue lines and semi-landmarks. It
consists of three larger moveable landmarks, which appear in red, white and yellow. Drag these
landmarks to define the base of the condyle patch. The two large blue landmarks indicate the
top and a corner of the patch. The projected patch renders with orange lines and semi-
landmarks and automatically adjusts when the condyle patch changes.
Right-click on the joint primitives overlay button and select Upside Down to change the
projection direction of the topmost point. Select Flip to flip the orientation and subsequent
point ordering of the joint. Select Align Avatar to Joint to align the axial to the joints three
control points. Select any of the three condyle patch landmarks from the Condyle Control
Points menu. The Snap condyle white landmark to sagittal slice command snaps the white
condyle landmark to the avatars current sagittal slice. Figure 25 shows an initially placed joint,
and Figure 26 shows the joint after adjusting the three condyle landmarks. The Landmark tab
allows for the adjustment of all the joints semi-landmarks.
Tutorial A: Joint Congruence Using a Joint Primitive, on page 71, explains how to use a joint
primitive for shape analysis.
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Figure 25: A joint consists of a condyle patch - blue - and a projected patch - orange. Moving the red,
white and yellow landmarks defines the condyle patch.
Figure 26: A joint after moving the condyle patch landmarks
Lengths: For measurement between two landmarks, enable landmark editing with the
icon. Select two landmarks, red and white, and click the icon to add the length primitive.
Lengths dont have names and cant be marked as missing. Figure 27 demonstrates the length
creation process.
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Figure 27: Image A shows selected red and white landmarks. Image B shows the created Length primitive.
Angles: An angle is defined by three or four landmarks. Enable landmark editing with the
icon. Select three landmarks - red, white and blue - or four landmarks -red, white, blue and
green, and click the icon to add an angle primitive. Angles dont have names and cant be
marked as missing. Figure 28 below shows a three and four landmark angle.
Figure 28: Image A shows red, white and blue selected landmarks. Image B shows an Angle created with
three landmarks. Image C shows red, white, blue and green selected landmarks. Image D shows an Angle
created with four landmarks defining two line segments denoted by red-white and green-blue landmark
pairs.
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Planes: A plane is defined by three or four landmarks. Enable landmark editing with the
icon. Select three landmarks - red, white and blue - or four landmarks - red, white, blue and
green, and click the icon to add a plane primitive. A four landmark plane is positioned at
the average of the landmarks. Planes dont have names and cant be marked as missing. Figure
29, seen below, shows a three and four landmark plane and how they render differently when
selected and unselected. In order to align the axial slice window to a plane, right click in the 3D
window or any slice window to bring up the popup menu, then go to Align Avatar to: ->
Planes: and select any plane in the list. Restore the avatar to its original alignment by
selecting Default in the Align Avatar to: list.
Figure 29: Image A shows red, white and blue selected landmarks. Image B shows a Plane created with
three landmarks. Image C shows the unselected Plane. Image D shows red, white, blue and green selected
landmarks. Image E shows the Plane created with four landmarks. Image G shows the unselected Plane.
Iso Value Association
When created, a primitive associates itself with the current iso value (i.e. the surface it is placed
on). After adding primitives, then creating a new iso value, those primitives become invisible.
Select the option View -> Show Primitives from Inactive Isosurfaces to show the primitives
from all isosurfaces. The primitives from the inactive isosurfaces render differently, seen below
in Figure 30. Primitives not associated with the current iso value are not editable. This allows
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you to extract multiple surfaces from a volumetric scan, such as "bone" and "skin," so that you
can place multiple sets of landmark primitives on the surfaces.
Figure 30: Primitives from a different iso value render in a faded color.
Combining and Splitting Landmark Points

Click the icon to enable combining and splitting landmarks.
To Combine: Select two landmarks - red and white- then click the icon to combine them.
This action preserves the red landmarks position as seen below in Figure 31 and Figure 32.
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Figure 31: Image A shows selected red and
Figure 32: Image A shows selected red and
white landmarks. Image B shows them after
white landmarks. Image B shows them after
being combined.
being combined.
To Split: Select a landmark thats already been combined with other landmarks, then click the
icon to split it. The split landmarks offset in the normal vectors direction, as seen below in
Figure 33 and Figure 34.
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Figure 33: Image A shows selected red
Figure 34: Image A shows selected red
landmark. Image B shows the result after
landmark. Image B shows the result after
splitting landmarks.
splitting landmarks.
Landmarks Tab
The landmarks tab, seen below in Figure 35, allows you to change primitives names and to
toggle their missing flag. Under Landmark information, select a primitive type (e.g., In Figure
35, Single Points is the selected primitive type) to see a list of all those primitives.
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Figure 35: Landmarks tab. Primitive types are shown along the left-hand side and manipulation of the
selected primitive is shown on the right-hand side.
Primitive ordering changes by selecting a primitive, then clicking on the Move Up or Move
Down buttons. Figure 36 demonstrates this below. The reordering customizes the primitives
export order. In Figure 36, when Point 11 moves up four times from its default position, placing
it at the front, it exports first. However, if instead Point 11 moves down four times, placing it at
the end, it exports last.
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Figure 36: Changing Order with Move Up and Move Down. Left image shows Point 11s initial position.
Middle image shows Point 11 moved up four spots from its initial position. Right image shows Point 11
moved down eight times from the top position.
Selecting Single Points under Landmark information enables you to edit the selected points' X,
Y and Z position, as seen above in Figure 35.
Selecting Curves or Patches under Landmark information allows you to set their semi-landmark
densities, flip their directions, set missing semi-landmarks, and name control points.
Set the density under Semi-landmark Density. Figure 38 compares the same
curve with different semi-landmark densities. Figure 41 does the same
comparison with a patch.
Flip the orientation with the Flip button under Direction, as seen in Figure 37
and Figure 40.
Patches can also rotate their first landmark indicator with the Rotate arrow
buttons as seen in Figure 40.
Select a primitive, then either left click or use the < and > buttons to select a
semi-landmark. Set it as missing by checking the Mark as missing box. Figure
39 and Figure 42 show a curve and a patch, respectively, with missing semi-
landmarks. Changing the semi-landmark density resets all semi-landmarks to
not missing.
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Rename control points by selecting a primitive, then selecting a control point
from the Control Points list (see Figure 43) and typing a new name in the
Control Point Name edit box (see Figure 44).
Figure 37: Curve editing options.
Figure 38: Curve semi-landmark density comparison
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Figure 39: Curve with missing semi-landmark renders as a broken blue line in the curve
Figure 40: Patch editing options
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Figure 41: Patch semi-landmark density comparison
Figure 42: Patch rendered with missing semi-landmarks
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Figure 43: Selecting a primitive lists its control points
Figure 44: Select a control to rename it. Unnamed control points are listed as "(Point #)".
Select Joints under Landmark information to adjust semi-landmarks in the joints patches, set
the joints dimensions and a name, and set each opposing patchs name. Figure 45 shows the
editing options available for joints.
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Set the dimensions of the joints patches under Semi-landmark Density.
Flip the orientation of the joint with the Flip button.
Turn the joint upside down with the Upside Down button.
Semi-landmark Group refers to the two patches, which can be renamed.
The < and > button next to the semi-landmark group name selects the previous
and next available patch. The selected semi-landmark group shows up in the 3D
window and allows editing its semi-landmarks.
Under Semi-landmark, the < and > buttons select the previous and next semi-
landmark in the group; the << and >> buttons skip to the first and last semi-
landmark in the group; and the Mark as missing check box sets the selected
semi-landmark as missing.
Under Control Points, select a point to rename it.
Figure 45: Joint edit options.
Figure 46: Adjust the joints patches
Figure 46 shows the addition of two slice windows when editing joints. Each window aligns to
the selected semi-landmark of the selected group. Click on a semi-landmark in the 3D view, or
use the < and > buttons under Semi-landmark, to select the semi-landmark. Using the
left/up and right/down arrow keys on the keyboard also moves through the semi-landmarks in
the group. Pressing the M key toggles the selected semi-landmark as missing.
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Figure 47: Left image shows a non-missing semi-landmark. The right image show a semi-landmark
marked as missing.
Semi-landmarks can only be moved in the slice window along the long dotted line. Reset the
positions of all the semi-landmarks in both patches by changing the joints dimensions, flipping
the joints orientation, turning the joint upside down, moving the condyle patch landmarks (red,
white or yellow), or moving the first two semi-landmarks, which appear as blue spheres in the
3D view, in the blue condyle patch.
The section Shape Analysis Tab, (see below), further explains how to add these joints to the
shape database under the sub section Add Specimen to Population.
Template Tab
Save a set of custom placed primitives to apply to other scans. Templates require placing a set
of anchor points on a new scan and matching those points to template anchor points in order to
apply the template. The template is applied using thin plate splines to allow smooth morphing.
The following guides show how to create a new template, then how to apply a template to a
new scan. The Edit Template section shows how to add lines to template points and update
other template attributes.
Create New Template

1. Load a new scan.
2. Add primitives (Single Points, Curves, Patches, etc).
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3. Go to the template tab (Figure 48).
Figure 48: Template tab
4. Click on New to start creating a new template (Figure 49).
Figure 49: Click the New button to begin creating a new template
5. The template edit window (Figure 50) allows adding anchor and auto-placed primitives
to the template. Anchor points, which can only be single points and/or curve points, are
the points required to be placed on a scan in order to apply a template. A minimum of 3
single point primitives or a curve with a minimum of 3 landmarks are required. Auto-
placed primitives are primitives automatically placed by the template.
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Figure 50: Template edit window
6. Select a primitive from the list and click on the >> button to add it to the template as an
anchor or auto-placed primitive (Figure 51).
Figure 51: Add the selected primitive to the template as an anchor or auto-placed primitive
7. Once all anchor and auto-placed primitives are set, click Save to save the template
(Figure 52).
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Figure 52: Save the template after setting all anchor and auto-placed primitives
8. The newly saved template is available in the Templates list (Figure 53). The template
file is saved in your My Documents\My Checkpoint Templates folder.
Figure 53: The new template is available in the Templates list
Apply Template
1. Load a new scan.
2. Use single point primitives to specify the specimen anchor points for the template. Only
single point primitives can be used for this step even if the anchor points on the
template originate from a curve primitive.
3. In the template tab, select the template to apply (Figure 54).
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Figure 54: Template selected. Preview of template on the left 3D window.
4. Select a point under Template Anchor Points and select the matching point under
Specimen Anchor Points (Figure 55). Click the > button to set the pair of points as
matched points (Figure 55).
Figure 55: The selected Template Anchor point is highlighted in the template preview 3D window (left).
The selected Specimen Anchor point is highlighted in the scan's 3D window (right).
Figure 56: All template anchor points matched with specimen anchor points
5. Click Apply (Figure 57).

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Figure 57: Apply the template after matching all anchor points
6. The template is now applied. Semi-landmarks in curves and patches will not project
onto the surface until all the auto-placed control points are adjusted by the user. These
points appear with animated spheres in the 3D window (Figure 58). Primitives
containing unadjusted landmarks will render their 2D glyphs with a small blue circle on
the upper right (Figure 59).
Unadjusted auto-placed points will update as landmarks are moved.
Figure 58: Auto-placed template landmarks rendered with animated blue spheres.
Figure 59: Primitives containing auto-placed template landmarks render their overlay glyphs with blue
circle on the upper right.
Edit Template
Edit the selected template by clicking the Edit button (Figure 60).
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Figure 60: Edit the template
Editing allows:
Renaming the template

Changing anchor primitives and auto-placed primitive ordering
Removing anchor and auto-placed primitives
Adding lines between points
Add a line by selecting two points in the 3D window (Figure 61). The selected points render in
orange and green. Selecting two points enables the Add Line button; clicking it will add the line.
Figure 61: Selected points render in orange and green. A line can now connect these points.
Every added line will have an accompanying overlay button (Figure 62). Left clicking it will select
the line. Pressing the delete key on the keyboard while a line is selected will delete it.
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Figure 62: The added line renders a dotted black and white line. The 2D overlay button renders on the
top left.
Update Template
Update the selected template to the current scan if the template was already applied (Figure
63). The update works even if the template was applied before loading the scan. This updates
landmark positions and/or primitive annotations and densities for curves, patches, and joints
(Figure 64). Densities are always updated, but annotations and landmark positions updates are
optional.
Figure 63: Click Update to bring up the update dialog
Figure 64: Update the template's landmark positions, names, and densities. Densities apply to curves,
patches, and joints.
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Landmarks Not on a Surface
Landmarks may appear off the surface after applying a template or adding single points in the
slice window, as seen below in Figure 65. Landmarks in the 3D window move when dragged
along a surface, which means a surface must be behind the landmark in order for it to move.
Figure 65: A single point and curve not on a surface
Trying to move a landmark without a surface behind it will select the landmark and rotate the
screen, which is not the desired action. In order to snap the landmarks on the surface, rotate
the surface so that it is behind the landmarks, like Figure 66 below. Then move each landmark
in order to snap it to the surface, see Figure 67 and Figure 68 below.
Figure 66: Image rotated so surface is behind the curve's points
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Figure 67: Curve's points snapped onto the surface
Figure 68: Single point landmark snapped onto the surface
Export Tab
Export landmarks and surfaces using this tab, as seen below in Figure 69. The sections below
detail the exporting process. All the exported volumes and surfaces retain their coordinate
space.
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Figure 69: Export tab. Volumes can be exported along the left-hand side. Surfaces can be exported in the
middle. Landmark points can be exported along the right-hand side.
Export Volumes
Refer to Figure 70 below. Select a file format from the list provided in Export format. The
Using these units attaches new units (i.e. mm, m, etc.) to the exported surface. The Filter
and Iterations options apply smoothing and sharpening filters to the exported volume. Higher
iterations reapply the filter the specified number of times. The Include Landmarks check box
toggles export of landmarks with the volume. Click the Export Volume or Export Reflected
Volume button, then select a directory and a name for the file and click Save to export. The
Volume export preview window renders the volume, which will be exported.
Figure 70: Export volume
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Export Surfaces
Refer to Figure 71 below. Select a file format from the list provided in Export format. The
Using these units attaches new units (i.e. mm, cm, etc.) to the exported surface. Leave the
setting 'default' as is to use the imported units. Use the Surface to export option to select
which isosurface to export if more than one iso value was used. The Include Landmarks check
box toggles export of landmarks with the surface. Click the Export Surface, or Export
Reflected Surface button, then select a directory and a name for the file and click Save to
export. The Surface export preview window renders the surface to be exported.
Figure 71: Export surface.
Refer to Figure 72 below. Click the Split Surface into Parts button to create a list of selectable
surface parts listed under Parts. Each part represents a section of the surface. Select a part
from the list to render the associated surface. Use 'shift' and left-click or ctrl and left-click to
select several parts from the list. The Select All button selects all the parts. The Invert
button inverts the current selection. For example, in the figure below, invert would unselect
Comp 0 and select all the other parts. Exporting only includes the selected parts.
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Figure 72: Surface with split parts listed
Export Landmarks
Refer to Figure 73 below. Select a file format from the list provided in Landmark export
format. Check the Allow Duplicates box to allow duplicate landmark points in the exported
file. Check the Apply Cropping to crop the exported primitives. All the points of a primitive
must be within the cropping bounds for it to remain in the exported point set. Select the iso
value under From Surface: to only export landmarks associated with it. Select All to include
the landmarks from all the iso values. Click the Export Landmarks button, then select a
directory and a name for the file and click Save to export. The window labeled Landmark
export preview shows the file format of the exported data. Data from all of the selected iso
values export together in the following order: single points, curves, patches. The direction of
the curves determines their export order (see Figure 23) in the primitives section. The rotation
and orientation of patches determines their export order (see Figure 24) in the primitives
section.
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Figure 73: Export landmarks.
Export Cropped Volumes and Surfaces

Enable the cropping lines with the icon. The lines appear in each slice window as blue
dashed lines, as seen below in Figure 74. Hovering over a crop line with the mouse highlights it
in yellow. Drag the crop line with a left-click to reposition it.
Once all crop lines are positioned, go to the Export tab. The preview windows will show the
cropped volume and surface. Select the exporting parameters and click the export or export
reflected button, as described in the above exporting sections, to save the cropped volume or
surface.
To change between exporting cropped data and uncropped data, enable and disable the
cropping lines with the icon.
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Figure 74: Slice window with crop lines shown in blue dashed lines
When the avatar is positioned outside of the cropping lines in any slice, the cropping lines will
disappear from another slice window. For example in Figure 75 below, the avatar, highlighted in
yellow, is positioned outside of the cropping bounds in the Axial and Coronal slice windows.
This causes the Sagittal slice window to not show the cropping lines because that current slice is
cropped.
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Figure 75: Avatar outside of cropping lines in Axial and Coronal slice windows causes the cropping lines to
not show in the Sagittal slice window.
Shape Analysis Tab

Perform shape analysis on populations of categorized specimens and export the results.
Figure 76: Shape analysis tab
Add Population: Click the + button, seen below in Figure 77, to pop up the Add Population
window (Figure 78 below). The window can create a new population or import one.
Remove Population: Click the - button to remove the current population.
Edit Population: Click the Edit button to rename the population.
Export Population: Click the Export button to export the current population. Select
populations using the combo box below Population. The population is exported in the file
format specified in the combo box next to the button.
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Import Specimen: Click the Import button to import one or more specimens.
Figure 77: Add, remove, and edit populations
Figure 78: Create or import a population
Checkpoint saves all populations upon exit or after clicking the icon. The files reside in My
Documents in a folder named My Checkpoint Shape Database. Each population is saved in an
individual file. Checkpoint automatically scans this folder and loads all population files upon
start up. These files can be shared with colleagues by copying them into their My Checkpoint
Shape Database folder. If the folder does not exist, create a new folder and name it My
Checkpoint Shape Database.
Add Specimen to Population: Click the + button (Figure 80 below), to add the selected scans
landmarks to the current population. Select a scan to add by clicking on its tab, which is below
the +, -, and Edit. Each added specimen must have the same number of landmarks as
those in the population. For example, if the first specimen added has 100 landmarks, then the
population will only accept additional specimens with 100 landmarks. If the selected scan has a
joint primitive, a pop up window appears to handle how the opposing surfaces are added to
separate populations, as seen in Figure 79.
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Figure 79: Add all primitives to the currently selected population or add a joint's semi-landmark groups to
separate populations
Select the joint to import from the list under Joints. Name the specimens that will hold the
associated semi-landmark group. Next, select the destination population for each specimen.
For example, in Figure 79, the semi-landmark group condyle will be added to a new specimen
named Specimen 1 and then added to condyle population, while the group fossa will be
added to a new specimen named Specimen 2 and then added to fossa population.
Alternatively, all primitives can be imported to the currently selected population by left clicking
the Import All Primitives radio button.
Remove Specimen: Select a specimen from the Specimens list and click the - button.
Edit Specimen: Select a specimen from the list and click the Edit button.
Figure 80: Add, remove, edit, or import a specimen in the current population
Stratifications
Stratifications allow categorizing of specimens within a population (refer to Figure 81 below).
Under Analysis Method, select Stratification to add, remove and edit population and
specimen stratifications. Initially, default stratifications fill the Population Stratifications list.
Each population contains a list of stratifications that can be assigned to any specimen within the
population.
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Add Population Stratification: Click the + button, located under the Population
Stratifications list, then enter the name for the stratification.
Remove Population Stratification: Select a stratification from the Population Stratifications

list and click the - button. Removing stratifications from a population will remove it from all
specimens within the population.
Edit Population Stratification: Select a stratification from the Population Stratifications list
and click the Edit button. Editing a stratification from a population will update the specimens
within the population that use the stratification.
Figure 81: The Condyle Population has the stratifications Normal, Diseased, Injured and Repaired,
which can all be used by the specimens within the population.
Add Specimen Stratification: Select a specimen from the population, then select a stratification
from the Population Stratifications list, then click the > (see Figure 82 below).
Remove a Specimen Stratification: Select a specimen from the population, select a stratification
from the Specimen Stratifications list, then click the < button.
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Figure 82: Added "Normal" stratification to the specimen "Pat02_l_condyle"
Shape Analysis: Average

The average shape analysis calculates the average specimen of a population. Under Analysis
method, select Average, as seen below in Figure 83. Each specimen in the population must
have had landmarks added in the same order for the analysis to function properly.
Figure 83: Calculate the average specimen of the selected population.
Filter Specimens: Use the Include and Exclude to filter specimens based on stratifications.
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Calculate Average Specimen: Click the Analyze button to calculate the average specimen for
the selected population.
Unselect Specimen: Click in the 3D window and press Space Bar.
The average specimen renders with red points, while the specimens render in grey, as seen
below in Figure 84. All specimens are rigidly aligned to the average specimen.
View different analysis results with the options under Result. These options include:
All: Renders the average and all specimens.
Average: Only renders the average specimen.
Specimens: Renders the specimens.
Selected Specimen: Renders the average specimen and the specimen selected under
Specimens.
Change the size of the points using the slider next to Size, which is to the right of the
Analyze button. Toggle between 2D square points and 3D spheres with the Render Spheres
check box. Toggle landmark annotations with the toolbar icon.
Figure 84: Average specimen shown with red points. All other specimens are rigidly aligned to the
average and render in grey.
Export the current Result in the format specified under Format, select the export units
under Units, then click the Export button.
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Shape Analysis: Generalized Procrustes Analysis
The Procrustes superimposition method calculates the Procrustes average specimen, which
removes scale from the specimens. Under Analysis method, select Generalized Procrustes
Analysis, (see below in Figure 85). Each specimen in the population must have had landmarks
added in the same order for the analysis to function properly.
Filter Specimens: Use Include and Exclude to filter specimens based on stratifications.
Calculate Procrustes Average Specimen: Click the Analyze button to calculate the Procrustes
average for the selected population.
Figure 85: Procrustes superimposition removes scale from specimens.
The analysis provides the Procrustes average, all specimens in Procrustes coordinates and
aligned to the Procrustes average, and all specimens aligned to the Procrustes average. The
Procrustes average renders in red and the specimens render in grey.
View different analysis results with the options under Result. These options include:
All Proc Coord: Renders the Procrustes average and all the specimens in Procrustes coordinates.
Proc Ave: Renders the Procrustes average.
Specimens Proc Coords: Renders all the specimens in Procrustes coordinates.
Selected Proc Coord: Renders the Procrustes average and the specimen selected under
Specimens.
Proc Ave and Specimens: Renders the Procrustes average and the specimens in their original
scale.
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Specimens: Renders the specimens in their original scale.
Selected Specimen: Renders the Procrustes average and the specimen selected under
Specimens in its original scale.
Export the selected Result in the format specified under Format, select the export units
under Units, and then click the Export button.
Shape Analysis: Joint Congruence

The joint congruence compares two populations with matching specimens and landmarks, and
calculates an average and distances between matching landmarks, such as the condyle and fossa
of the temporomandibular joint. Under Analysis method, select Joint Congruence, as seen
below in Figure 86.
Figure 86: Joint congruence calculates an average of two matching populations and provides landmark
distance information
Set Matching Population: Select a second population to match with under Matching
Populations, (Figure 87 below). The list includes populations that share the same number of
specimens and the same number of landmarks for each specimen. The matching population
must have had landmarks added in the same order as the selected population for the analysis to
function properly. For example, in Figure 87, the first point added to the specimens in the
condyle population match with the first point added to the specimens in the fossa population.
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Figure 87: Select a matching population and set matching specimens to perform the analysis
Specimen Matching: Click the Edit Specimen Matching button to specify which specimens
from each population match with each other, as illustrated in Figure 88 below. The list initially
fills with a default matching for specimens. Click the Reset button to remove all matches or to
select an individual match and click the << button to remove that match. For example, Figure
89 shows all specimen matches removed. Select one specimen from each population, then click
the >> button to add them as matching. The matching depends on the order the landmarks
were added in each specimen. Click Ok to save the matches. The matches remain saved even
after closing Checkpoint. The analysis only uses matched specimens and excludes any
unmatched specimens.
Figure 88: Edit specimen matching window sets initially sets default matches
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Figure 89: All specimens unmatched
Filter Specimens: Use the Include and Exclude options to filter specimens based on
stratifications.
Methods: Select a method to use for analysis under Method. The method sets the analysis
performed by the Analyze command. Average calculates the average specimen.
Procrustes performs the generalized Procrustes analysis.
Perform Analysis: Click Analyze to calculate the specified type of average specimen for the
matched populations.
View different analysis results with the options under Result. Using the Average method,
these options include:
All: Renders the average in red and orange with a line connecting the matching points. The
specimens render in grey, as seen below in Figure 90.
Figure 90: Average specimen shows the matched landmarks by connecting them with lines
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Average: Renders the average in red and orange with a line connecting the matching points.
Selected Specimen: Renders the average and the selected specimen with its matching
specimen. The selected specimen renders in yellow and blue.
All Specimens Spacing: Renders all specimens with lines connecting the matching landmarks.
The selected specimen renders in yellow and also renders an annotation with the distance
measurement.
Average Spacing: Renders the average and an annotation with the distance measurement.
Selected Spacing: Renders the average, the selected specimen with the matching specimen and
lines connecting the matching landmarks, and an annotation with the distance measurement,
(see Figure 91 below).
Figure 91: Selected specimen and matching specimen with spacing annotations
Using the Procrustes method, the Result options include:
All Proc Coords: Renders the Procrustes average in red and orange. The specimens render in
grey.
Proc Ave: Renders the Procrustes average.
Selected Proc Coord: Renders the Procrustes average and the selected specimen and its
matching specimen in Procrustes coordinates.
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Proc Ave and Specimens: Renders the Procrustes average and the specimens with their original
scale.
Selected Specimen: Renders the Procrustes average and the selected specimen and its matching
specimen in their original scale.
All Proc Coord Spacing: Renders the Procrustes average and all specimens in Procrustes
coordinates with lines connecting the matching landmarks.
Proc Ave Spacing: Renders the Procrustes average and annotations showing the distance
between the matching landmarks.
Selected Proc Coord Spacing: Renders the Procrustes average, the selected specimen with the
matching specimen in Procrustes coordinates and lines connecting the matching landmarks, and
annotations showing the distance between the matching landmarks.
All Specimens Spacing: Renders the Procrustes average and the specimens in their original scale
with lines connecting the matching landmarks.
Selected Spacing: Renders the Procrustes average, the selected specimen with the matching
specimen in their original scale and lines connecting the matching landmarks, and annotations
showing the distance between the matching landmarks.
Select a format and units for export under Format and Units. Export the selected Result
using one of the non-spacing options to merge the matched specimen into a single specimen
and export the landmark coordinates. For example, using the matches from Figure 88 results in
four merged specimens, where the condyle populations specimens landmarks represent the
first half of the merged specimens and the fossa populations specimens landmarks represent
the second half. Export the spacing results in the following with the selected Result option:
All Specimens Spacing: Exports the averages spacing if using the Average method or the
Procrustes averages spacing if using the Procrustes method, and exports all specimens
spacing in their original scale.
All Proc Coord Spacing: Exports the Procrustes averages spacing and all the specimens spacing
in Procrustes coordinates.
Average Spacing: Exports the averages spacing.
Proc Ave Spacing: Exports the Procrustes averages spacing.
Selected Proc Coord Spacing: Exports the Procrustes averages spacing and the selected
specimens spacing in Procrustes coordinates.
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Selected Spacing: Exports the averages spacing if using the Average method or the Procrustes
averages spacing if using the Procrustes method and the selected specimens spacing in its
original scale.
Warping Tab
The warping tab (Figure 92) provides a method to warp surfaces and volumes. Each surface,
volume, and population to be included in a warp must contain the same set of primitives, which
must be placed in the same order. Once the primitives are set, the warping tab enables the
following procedures:
Warp two surfaces to a Procrustes average surface

Warp a surface to a Procrustes average using a populations average, a populations
Procrustes average, or a specific populations specimen
Generate an average or Procrustes average volume from a set of volumes
Warp a set of volumes to the average or Procrustes average of the volume set
Figure 92: The warping tab
Surface Warping: Two Surfaces
Begin surface warping by loading two scans. Each scan must have the same set of primitives
placed on them. Click the Edit Warp button (Figure 93) to pop up a window for setting warp
targets.
Figure 93: Click the 'Edit Warp' button to set warp targets
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Under the section Specimen A (Figure 94), click on the combo box next the Open Specimen
and select one the open scans.
Figure 94: Select an open specimen as the warp target
Under the section Specimen B (Figure 95), click on the combo box next the Open Specimen
and select the other open scan.
Figure 95: Specimen B can either be an open specimen or be based from a population
Both warped surfaces will render in the main window of the warp tab. The slider adjusts the
weight each specimen has towards the average (Figure 96). The weight is displayed as a
percentage next to From A and To B. Change the rendered result with the Result combo
box (Figure 97). The combo box displays and A or B next to the name of the specimen to
indicate which is specimen A and specimen B (Figure 98). Export the current result surface(s) by
clicking the Export button.
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Figure 96: Move the slider to adjust the weight each specimen has on the Procrustes average
Figure 97: Select the result to render and export
Figure 98: Specimen A (left) and specimen B (right)
Surface Warping: A Surface and Population
Begin warping a surface to a population by loading in a scan and placing the same set of
primitives on it as those in the population of interest. Click the Edit Warp button and set
Specimen A to the current scan. Select a population for Specimen B (Figure 99).
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Figure 99: Set a population for Specimen B
Within the population the following options become available:
Specimen: Select a specific specimen from the population for Specimen B.

Analysis: Select a population analysis result for Specimen B. This is either the
populations average or a Procrustes average. The analysis provides options to include
or exclude population specimens from the analysis based on stratifications.
Volume Warping and Average
Volume warping generates an average or Procrustes average from a set of volumes and warps
each volume from the set to that average. The warp can be excluded so only an average or
Procrustes average is generated and exported.
Begin by loading a volume scan, placing an ordered of primitives, save the scan, and then close
the specimen. Repeat this step for each volume scan that will be part of the warp. Once all
volumes have been saved and closed, go the warp tab and click the Volume Warp button
(Figure 100).
Figure 100: Click the "Volume Warp" button the pop up the volume warping window
In the warp volume window, drag and drop the Checkpoint (*.ckpt) files into the Specimens
list box (Figure 101).
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Figure 101: Drag all the Checkpoint files in the "Specimens" list box
Alternatively, the + button can be used to navigate to a Checkpoint file to add. Remove a
Checkpoint file from the list by selecting it, then clicking the - button. Set a folder to receive
the exported output volumes (Figure 102).
Figure 102: All generated volumes are exported to the specified folder
Select a process under Average and Warped Volumes to perform on the set of volumes, then
click Warp to begin the process. The processes include:
Only the Population Average (default): Generate and export only the average volume.
Only the Procrustes* Average of the Population: Generate and export only the
Procrustes average volume.
Only the Specimen Warps to the Population Average: Generate the average volume,
warp the specimens to the average, and export the warped specimen volumes.
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Only the Specimen Warps to the Procrustes* Average of the Population: Generate the
Procrustes average volume, warp the specimens to the average, and export the warped
specimen volumes.
The Population Average and the Specimen Warps: Same as Only the Specimen Warps
to the Population Average but also exports the average volume.
The Procrustes* Average of the Population and the Specimen Warps: Same as Only
the Specimen Warps to the Procrustes* Average of the Population but also exports the
Procrustes average volume.
The exported warped specimens will prepend the text Warped to the file names. For example,
the warped file name for anon00 will be Warped anon00. The file name for the average and
Procrustes average will take the folders name. For example, if the export folder is call
C:\Temp\VolumeWarp, the averages file name will be VolumeWarp Average and the
Procrustes averages file name will be VolumeWarp Procrustes Average.
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Figure 103: Population Average Methodology. The steps used to compute the population average are
described above.
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Tutorial A: Joint Congruence Using a Joint Primitive
The following explains how to set up specimens for both populations used in joint congruence
using a joint primitive. The example creates condyle and fossa specimens of the
temporomandibular joint (TMJ) for their respective populations from a joint primitive. The
tutorial includes:
1. Loading a CT scan and using cropping to isolate a region of interest around the TMJ.
2. Exporting the isolated condyle and fossa volume.
3. Using right-to-left reflection for symmetry.
4. Adding and adjusting the joint primitive.
5. Adding the joint primitives patches to shape populations as specimens.
6. Analyzing the matching specimens using joint congruence.
Load Scan and Export Volume
1. Load a CT scan of a head. For this example, the scan includes both the fossa and
condyle.
2. Use the cropping lines to isolate the region of interest, as seen below in Figure 104.
Figure 104: Cropped volume isolating the condyle and the fossa
3. In the export tab, click on Export Volume to save the cropped volume. To export the
reflected volume, click on Export Reflected Volume.
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Placing the Joint Primitive
1. Load the exported volume.
2. In the surface tab, select an iso value that produces surfaces without holes in the
condyle and fossa.
3. Click the button, then hold shift and left-click on the condyle to add the joint
primitive (see Figure 105 below).
Figure 105: Joint primitive added to condyle
4. Move the red and yellow control points to the medial and lateral sides of the condyle, as
seen below in Figure 106.
Figure 106: Red and yellow control points moved to medial and lateral sides of the condyle
5. Optionally, to restrict the condyle white point to a plane that keeps this point
equidistance from the lateral points, first, right-click in the 3D or any slice window to
bring up the pop menu and select Align Avatar to: -> Joints -> Joint. This aligns the
avatar to the joint, placing it at the midpoint between the lateral red and yellow points
and aligning the sagittal slice perpendicular to the lateral points. Next, right-click on the
joints overlay button and select the Snap condyle white landmark to sagittal slice
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command, which projects the condyle white point to the sagittal slice defined by the
avatar, and also selects the condyle white point. Finally, use the sagittal slice window to
move the condyle white point.
Adjusting the Joint Primitive
1. In the landmarks tab, select the joint primitive.
2. Set the name and dimensions.
3. Toggle the volume or surface with the or buttons to verify that the top of the
patch is on the top of the condyle, as seen in Figure 107. If the patch is upside down, as
seen in Figure 108, then click the Upside Down button under Direction.
Figure 107: Verify condyle patch direction
Figure 108: Upside down condyle patch.
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4. Use the Flip button to swap the point ordering, which is seen with the swapped yellow
and red control point positions. This example places the yellow point on the lateral
condyle position, and the red point on the medial condyle position.
Adjusting Semi-Landmarks
1. Rename the condyle patch under Semi-landmark Group (see Figure 109 below).
Figure 109: Naming semi-landmark groups.
2. Drag the semi-landmark point in the slice window to adjust its position. The semi-
landmarks movement is restricted to the long dotted line, as seen in Figure 110.
Figure 110: Slide the semi-landmark along the long dotted line
3. Move to the next semi-landmark with the right arrow key on the keyboard or the >
button under Semi-landmark. Toggle a semi-landmark as missing by selecting a slice
window or 3D window and pressing the M key, or by clicking the Mark as missing
check box.
4. Once all semi-landmarks in the condyle patch have been adjusted, click the < or >
button under Semi-landmark Group, and repeat the above process for the fossa.
Create Populations and Add the Joint Primitive
1. In the shape analysis tab, add two new populations, one named 5x5 Condyle
Population and a second named 5x5 Fossa Population.
2. Click the + button under the list of specimens to pop up the joint import window, as
seen in Figure 111.
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Figure 111: Add the selected joint's semi-landmark groups to separate populations
3. Select the joint TMJ from the list. Name the specimen for each semi-landmark group.
4. Select a population under Import to Population to import each of the specimens.

Select the condyle population for the condyle semi-landmark group, and the fossa
population for the fossa semi-landmark group. Click Ok to import.
Joint Congruence Analysis
1. After adding more joint primitives to the populations, the shape analysis can proceed.
Select Joint Congruence under the Analysis method.
2. Select the population to match with the Matching Population. As seen below in Figure
112, select the 5x5 Condyle Population to match with the 5x5 Fossa Population.
Figure 112: Joint Congruence Analysis
3. Click Edit Specimen Matching to confirm the default matching or edit them. Click
Ok to save the matches. These matches will remain even after closing Checkpoint or
even after matching these specimens with another populations specimens.
4. Select a method for the analysis. Either Average or Procrustes, then click the
Analyze button. The Procrustes method performs the generalized Procrustes
analysis.
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Exporting Results
1. Using the Average method for the analysis provides multiple results under Result,
which can then be viewed and exported.
2. To export a csv file with the landmarks of the rigidly aligned matching specimens, select
All under Result, then select CSV under Format, and then click Export. Each
row in the csv file lists the matched specimens with the name Specimen A : Specimen
B, which is followed by the xyz landmark coordinates of Specimen A then the xyz
landmark coordinates of Specimen B.
3. To export a csv file with the distances between the matching landmarks of matching
specimens, select All Specimens Spacing under Result, then select CSV under
Format, and then click Export. Each row in the csv file lists the matched specimens
with the name Specimen A : Specimen B, which is followed by the distances between
the matched landmarks. The file identifies the matched landmarks used for each
distance at the top of each column as Mark A : Mark B.
Tutorial B: Joint Congruence with Two Patches

The following explains how to set up specimens for both populations used in joint congruence
without using a joint primitive. The example creates condyle and fossa specimens of the
temporomandibular joint (TMJ) for their respective populations. The tutorial includes:
1. Loading a CT scan and using cropping to isolate a region of interest around the TMJ.
2. Exporting the condyle and fossa surfaces.
3. Using right-to-left reflection for symmetry.
4. Matching landmarks on both surfaces.
5. Adding surface landmarks to shape populations as specimens.
6. Analyzing matching specimens using joint congruence.
Load Scan and Export Surfaces
1. Load a CT scan of a head. For this example, the scan includes both the fossa and
condyle.
2. In the surface tab, select an iso value that produces surfaces without holes in the
condyle and fossa.
3. Toggle the crop lines to isolate the region of interest, as seen below in Figure 113.
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Figure 113: Left condyle and fossa cropped surface
4. In the export tab, click the Split Surface into Parts button.
5. Select the part or parts that only include the condyle, then click Export. From the list
of parts, Comp 0 has the fossa (see Figure 114 below), and Comp 1 has the condyle,
(Figure 115 below). Select Comp 0 and click the Export Surface to save the fossa,
then select Comp 1 and click Export Surface to save the condyle. This region is of
the patients left condyle and fossa, so when adding the patients right condyle and
fossa use the Export Reflected Surface to take advantage of symmetry between both
sides and maintain orientation between scans. If the listed parts contained the fossa
connected with the condyle, then go back to step 2 to select a better iso surface.
Figure 114: Fossa surface component
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Figure 115: Condyle surface component
Add Landmarks to Surfaces
1. Select the fossa scan and add landmarks, as seen below in Figure 116.
Figure 116: Fossa with landmarks
2. Select the condyle scan and add landmarks in the same order as the fossa, as illustrated
below in Figure 117. The first landmark added to the condyle will match with the first
point of the fossa. If the order is incorrect, go to the Landmarks tab and use the
Move Up and Move Down buttons to adjust the order of the landmarks.
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Figure 117: Condyle with landmarks
3. If you use patches for both scans instead of single points, (as seen below in Figure 118),
then use the Landmarks tab to match orientation and starting points. Toggle on
rendered surfaces to ease aligning the scan with each other, as seen below in Figure
119. Once aligned, toggle off the rendered surfaces and use the Flip button to match
the orientation and the Rotate arrows to match the starting point, as depicted in
Figure 120 below.
Figure 118: Condyle and fossa scans shown side by side, each with a patch.
Figure 119: Condyle and fossa scans aligned with each other.
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Figure 120: Condyle and fossa patches with matching orientation and starting points
Create Populations with Specimens
1. In the shape analysis tab, add two new populations, one named Condyle Population
and a second named Fossa Population.
2. Select the Condyle Population, then select the condyle scan by clicking on its tab, then
add the specimen. The pop up window will have the name of the scan by default to
help confirm that the correct scan is selected (see below in Figure 121).
Figure 121: Adding specimen to condyle population
3. Select the Fossa Population, then select the fossa scan, and then add the specimen.
4. Each population now contains one specimen each. Repeat the process of loading scans,
exporting components, and adding landmarks to obtain more specimens to add to each
population.
Joint Congruence Analysis
1. After adding more specimens to the populations, the shape analysis can proceed. Select
Joint Congruence under the Analysis method.
2. Select the population to match with the Matching Population. As seen below in Figure
122, select the Fossa Population to match with the Condyle Population.
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Figure 122: Condyle population matched with the fossa population
3. Click Edit Specimen Matching to confirm the default matching, or edit them. Click
Ok to save the matches. These matches will remain even after closing Checkpoint or
after matching these specimens with another populations specimens.
4. Select a method for the analysis. Either Average or Procrustes, then click the
Analyze button. The Procrustes method performs the generalized Procrustes
analysis.
Exporting Results
1. Using the Average method for the analysis provides multiple results under Result,
which can then be viewed and exported.
2. To export a csv file with the landmarks of the rigidly aligned matching specimens, select
All under Result, then select CSV under Format, and then click Export. Each
row in the csv file lists the matched specimens with the name Specimen A : Specimen
B, which is followed by the xyz landmark coordinates of Specimen A, then the xyz
landmark coordinates of Specimen B.
3. To export a csv file with the distances between the matching landmarks of matching
specimens, select All Specimens Spacing under Result, then select CSV under
Format, and then click Export. Each row in the csv file lists the matched specimens
with the name Specimen A : Specimen B, which is followed by the distances between
the matched landmarks. The file identifies the matched landmarks used for each
distance at the top of each column as Mark A : Mark B.
Checkpoint File (*.ckpt)

The Checkpoint file stores all the landmarks, primitives, templates, and the image data file name
and is created after clicking the save button. The data is stored as plain text and can be viewed
81
in a text editor. The Checkpoint file must be in the same folder as the image data file (ply, nii,
etc.). Renaming the image data file will prevent the Checkpoint file from finding it.
Customer Support
If you have questions or comments regarding this software, please contact customer support
through our website: https://www.stratovan.com/support
Or by emailing: support@stratovan.com
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User Manual

February 23, 2017

Login Screen .................................................................................................................................................. 4

Internet Updates ........................................................................................................................................... 6

Specimen Tab ................................................................................................................................................ 6

Image Stacks ................................................................................................................................................. 8

Image Viewing Layout ................................................................................................................................. 11

Volume Tab ................................................................................................................................................. 14

Surface Tab ................................................................................................................................................. 15

Landmark Primitives ................................................................................................................................... 20

Combining and Splitting Landmark Points .................................................................................................. 27

Landmarks Tab ............................................................................................................................................ 29

Template Tab .............................................................................................................................................. 37

Landmarks Not on a Surface ....................................................................................................................... 45

Export Tab ................................................................................................................................................... 46

Export Volumes ........................................................................................................................................... 47

Export Surfaces ........................................................................................................................................... 48

Export Landmarks ....................................................................................................................................... 49

Export Cropped Volumes and Surfaces....................................................................................................... 50

Shape Analysis Tab ...................................................................................................................................... 52

Shape Analysis: Average ............................................................................................................................. 56

Shape Analysis: Joint Congruence............................................................................................................... 59

Warping Tab ................................................................................................................................................ 64

Tutorial A: Joint Congruence Using a Joint Primitive ................................................................................. 71

Tutorial B: Joint Congruence with Two Patches ........................................................................................ 76

Checkpoint File (*.ckpt) .............................................................................................................................. 81

Customer Support ....................................................................................................................................... 82

Figure 1: Checkpoint login screen

Figure 3: Set up node lock to avoid Internet-based login

Volume Surface Landmarks Surface Volume

DICOM PLY CSV PLY NifTI

TIFF/JPG Image OBJ Morphologika OBJ FITS

Figure 9: Load in the image stack with "MyImageStack.ckpt"

Move Slices: Right click and drag in a slice window.

Move 3D Volumes/Surfaces: Right click and drag in the 3D window.

Volumetric rendering is dependent on your computer's video hardware. We recommend using

Landmark Measurement Icons

Landmark Joining Icons

View Option Icons

: Enable or disable lighting for volumetric data. Disable to improve performance.

: Show or hide the surface mesh.

: Show or hide cropping lines.

: Enable or disable a 3D cut-away at the avatars position

: Decrease the size of landmarks and semi-landmarks.

: Increase the size of landmarks and semi-landmarks.

: Set the surface meshs opacity. Set to 100% to improve performance.

: Show or hide landmark points.

: Show or hide semi-landmark labels.

: Show or hide directions of curves and patches.

: Show or hide the bounding box.

: Change background color to white or black.

User Interface Font Icons

: Increase applications font size.

: Decrease applications font size.

: Set application font size to default.

: Info about Stratovan Relay TM.

: Undo/redo the most recent operation.

Select Landmarks: Left-click a landmark to select it.

Figure 21: Single point with normal vector

Figure 23: Curve direction indicated by arrows.

Figure 24: Patch orientation indicated by circular swoosh

Figure 26: A joint after moving the condyle patch landmarks

Iso Value Association

Combining and Splitting Landmark Points