Markers can be placed on any visible surface at any orientation. Accuracy
of placement is improved if the image is rendered at high resolution; either
by use of the [hires] option or by zooming the region of interest with
the [resize] option. Maximising the window does NOT improve measurement
accuracy.
Markers are placed by clicking the left mouse button over the object. The marker can be dragged around on the surface until the button is released (fine adjustment of marker position with the cursor keys is also possible if the move marker mode is selected - press enter to fix the new position). Two styles of interaction are supported: the first shows a simple cross where the marker will be placed, the other also shows the surface curvature by showing horizontal (red) and vertical (blue) profiles across the surface. These can assist in the correct placement of markers.
When placing a marker, a blue cross is displayed, indicating that the marker is ON the surface. If the rendering threshold is changed, the marker will no longer be on the surface. If it is more than the size of a data pixel away from the displayed surface the colour of the cross is changed to green. Markers added in the 3D reslice mode are very likely to be displayed in green as they are unlikely to be placed exactly on a surface.
When the surgical
simulation mode is used, to move objects around relative to each other,
the markers will not move with any of the objects. The markers always remain
in the original frame of reference. Adding corresponding markers after
repositioning an object permits the calculation of the resulting positional
change.
A Measurements window is displayed:-
The
window initially displays x, y, z co-ordinates of the markers in absolute
measurements mode; where x=0, y=0, z=0 is at the left, front, top corner
of the data in the initial orientation. Units are mm (provided that the
header file contains valid information!).These co-ordinates are viewpoint
independent and will not change if the view is rotated or shifted. If the
screen measurements mode in the Orient menu is checked, then
co-ordinates are displayed in the frame of reference of the current view
with 0,0,0 at the centre of rotation. These co-ordinates will change with
viewpoint. If the user defined measurements mode in the Orient
menu is checked, then co-ordinates can be displayed in a frame
of reference defined by the user. These co-ordinates will not change
with viewpoint. If a reference point is selected,
the display changes to show distances from each marker to the reference
marker. Solid angles (in degrees) and distances
to a reference plane can also be displayed. The volume or surface area
of the currently displayed object may be calculated by buttons in the options
menu. The accuracy of ALL measurements depends upon the validity of the
dimensions found in the data header file. NOTE: If an object is moved with
the editing facilities, any markers placed
on its surface will NOT move with the object but will stay in their original
location. Adding a new marker after editing allows measurement of the change
in position at the location.
| File | Load Markers from file | Reads marker locations from a .LAN file which has been previously saved |
| Save Markers to file | Writes marker locations to a .LAN file which can be re-loaded later or writes the window text to a .TXT file for export. The type of save is selected from the file save menu. There is also a .stl compatible lan mode. When data are saved in .stl format a different frame of refence is used. If the user wants landmarks compatible with the .stl file, this mode should be used. Landmarks saved in .stl compatible mode will NOT load correctly into this voxel software. | |
| Markers to clipboard | Writes marker locations in text format to the windows system clipboard. They can be pasted from the clipboard into other software packages. | |
| Orient | absolute measurements | When checked (default) x,y,z co-ordinates are displayed in data space with 0,0,0 at the left (x), front (y) , top (z) corner of the data space in the initial view. In the conventional CT slice view (from below) x is across the slice (left to right), y is down the slice (top to bottom), z is out through the stack of slices (top slice to bottom slice). |
| screen measurements | When checked x,y,z co-ordinates are displayed relative to the current view with 0,0,0 at the centre of rotation (and at the centre of the window).The X-axis is horizontal with negative values to the left. The Y-axis is vertical with negative values at the top. The Z-axis is out of the screen with negative values at the back. Rotating or shifting the viewpoint will change the co-ordinates displayed for a marker. | |
| user defined measurements | When checked x,y,z co-ordinates are displayed in a user definable space. | |
| Ref. point to centre | Shifts the view to put the reference point marker at the centre of rotation | |
| Ref. line vertical | Rotates the view so that the reference line appears vertical on the screen, but is not necessarily parallel to it. | |
| Ref. line horizontal | Rotates the view so that the reference line appears horizontal on the screen, but is not necessarily parallel to it. | |
| Ref. line in screen | Rotates the view so that the reference line becomes parallel to the screen. | |
| Ref. plane vertical | Rotates the view so that the reference plane appears vertical on the screen. | |
| Ref. plane horizontal | Rotates the view so that the reference plane appears horizontal on the screen. | |
| Ref. plane in screen | Rotates the view to put the reference plane parallel to the screen. | |
| Ref. plane standardised | Rotates the view to put the reference plane parallel to the screen and the reference line parallel to the screen x-axis. | |
| Ref. plane 2 standardised | Rotates the view to put the normal to the reference plane parallel to the screen x-axis and the reference line pointing out of the screen. | |
| Meas | Radius of curvature |  A
dialog box is displayed allowing the user to select 3 markers. The radius
of curvature of a circular arc passing through the 3 markers is calculated. |
| Line - line information |  A
dialog box is displayed allowing the user to select 4 markers. The solid
angle (in 3 dimensions) between the two selected lines is calculated. The
angle subtended by projecting the two lines onto the plane of the image
is also calculated. This projected angle is viewpoint dependent. Selecting
A-B and A-B again will give a solid angle of 0 degrees/radians. Swapping
the order of points on one line (A-B and B-A) will give a solid angle of
180 degrees. Also displayed are the locations on each line of the nearest
point to the other line. Markers can be added at these locations by clicking
on the relevant buttons. The shortest distance between the lines is also
shown. A marker added halfway along this line is at the location nearest
to both lines.When the solid angle is close to 0 or 180 degrees, the lines
are nearly parallel. Under these conditions the marker locations should
not be relied upon because small errors in line position can cause large
movements of these locations. |
|
| Angle between planes |  A
dialog box is displayed allowing the user to select 6 markers. The angle
between the two selected planes is calculated. Selecting A-B-C and A-B-C
again will give an angle of 0 degrees/radians. Swapping the order of points
on one triangle (A-B-C and A-C-B) will give an angle of 180 degrees.The
angle subtended by projecting the two plane normals onto the image is also
calculated. This projected angle is viewpoint dependent. |
|
| Line - plane information |  A dialog box
is displayed allowing the user to select 5 markers. The solid angle (in
3 dimensions) between the selected line and plane is calculated. The angle
subtended by projecting the line onto the plane of the image and the line
of intersection of the plane of the screen and the chosen plane is also
calculated. This projected angle is viewpoint dependent. The point of intersection
of the line and plane is shown in absolute co-ordinates. A marker may be
added at this location. When the solid angle is close to 0 or 180 degrees,
the line is nearly parallel to the plane. Under these conditions (as shown!)
the intersection is an unreliable location. |
|
| Add Marker at XYZ | This allows the user to add a marker at an arbitrary x,y,z position in the current frame of reference. | |
| Add mid-point marker | A dialog box is displayed allowing the user to select 2 markers. Pressing ok will add a new marker at the mid-point between the chosen markers. | |
| Fit LSQ line to markers | 
This option allows the user to fit the best (Least Square error) line through the set of points selected in the left hand window of the dialog box. The RMS error of the points to the line is reported. After Calculation, extra landmarks can be added on this line using the buttons on the right side of the dialog box or, by double clicking on any marker in the selection windows, a new marker can be added on the line at the nearest point to the clicked marker. Individual distances, from each point to the fitted line, are diplayed in the selection windows, adjacent to each marker name, after fitting. There is also an extra option to remove the worst fitting point from the list and re-calculate. |
|
| Fit LSQ plane to markers | This is similar to the option above but fits the best plane to the selected set of points. After the plane has been defined, double clicking on any marker in the selection windows will add a new marker on the plane at the nearest point to the clicked marker. Individual distances, from each point to the fitted plane, are diplayed in the selection windows, adjacent to each marker name, after fitting.There is also an extra option to remove the worst fitting point from the list and re-calculate.The data set can be rotated to align the fitted plane with the plane of the screen. | |
| Fit LSQ sphere to markers | This is similar to the option above but fits the best sphere to the selected set of points. After the sphere has been defined, double clicking on any marker in the selection windows will add a new marker on the fitted sphere at the nearest point to the clicked marker. Individual distances, from each point to the fitted sphere, are diplayed in the selection windows, adjacent to each marker name, after fitting.There is also an extra option to remove the worst fitting point from the list and re-calculate. | |
| Fit LSQ circle to markers | This is similar to the option above but fits the best circle to the selected set of points. This has to be a two stage process. First a best fit plane to the points is found. Temporary copies of the selected points are moved into this plane before finding the best fit circle. Individual distances, from each point to fitted circle, are diplayed in the selection windows, adjacent to each marker name, after fitting.There is also an extra option to remove the worst fitting point from the list and re-calculate. | |
| Length of polyline | 
This calculates the length of a number of straight line segments between markers. The first measure, ordered length joins all of the chosen markers in their alphabetic order. Click on the show button to see the measured line segments. The loopback measurement also adds in the line segment from the last marker to the first marker. The nearest neighbour option will not necessarily use all of the selected makers. Use the show button to see the path actually used. Nearest neighbour finds the pair of markers which are farthest apart and joins lines between these and their nearest neighbours, using the markers in any appropriate order. |
|
| Del | Select Markers to Delete | Displays a popup allowing the user to select a list of markers to be deleted. |
| Delete All Markers | Clears the entire marker list | |
| UnSet | Clears plane, line & point attributes (one per click) | |
| ? | This Help | |
If the profile mode is enabled (see styles), then clicking on a marker in the measurements window will cause the profiles for that marker to be displayed. Left clicking on a marker first brings up brings up a selection menu (as shown in the sample window above):
| cancel | do nothing in this menu (except show profiles at the selected marker) |
| move | allows the chosen marker to be moved on the main screen. It can either be dragged by pressing the left mouse button or fine adjusted with the cursor keys. Either releasing the left mouse button or pressing <enter> will fix the new marker position. |
| delete | deletes the chosen marker, moving all subsequent marker tags back a character |
| insert | moves this and all subsequent markers forward a character, allowing the insertion of a new marker |
| set ref point | This sets the chosen marker to be a reference point and changes the display to show distance from each point to the chosen reference. The marker cross changes colour to red. |
| set ref line | If a reference point (as above) has been defined, this allows a second marker to be used to define a reference line. each angle (mark-RefPt-RefLine) is shown. The reference line is drawn on the image. |
| set ref plane | If a reference line has been defined (as above), this allows a third marker to be used to define a reference plane with the three chosen markers. Perpendicular distances from each marker to the plane are shown. When (refPt, RefLine, RefPlane) define a clockwise triangle, negative distances are to points nearer to the viewer than the plane. The reference triangle is drawn on the image. |
| put to centre | Clicking on this moves the data so that the marker is at the centre of rotation. This has no effect on the reported absolute marker positions but will change the screen based marker values. This option is useful for centreing a region of interest prior to examination at high magnification in the 3D reslice mode. |
| Vert prof to clip | Writes the x,y,z co-ordinates of the vertical profile, through the nearest screen pixel to the position of the selected marker, to the windows system clipboard in text format. The frame of reference of the values will depend upon the selected mode. They can be pasted from the clipboard into other software packages. |
| Horiz prof to clip | Writes the x,y,z co-ordinates of the horizontal profile, through the nearest screen pixel to the position of the selected marker, to the windows system clipboard in text format. The frame of reference of the values will depend upon the selected mode. They can be pasted from the clipboard into other software packages. |
| Set XYZ value | This allows the user to set the chosen marker to an arbitrary x,y,z position in the current frame of reference. |
If the user defined measurements option
is checked, then right clicking on a marker in the measurements window
will bring up a different selection window 
allowing
the user to define their own frame of reference for the co-ordinates displayed
by the marker window. This has a number of different controls for modifying
the frame of reference.
The first option, Set user orientation & position, sets a frame of reference by copying the current screen settings. This re-defines both orientation and the position of the origin.
The second option, set user orientation, allows the definition of orientation by using two markers to define the x-axis direction and a third to define a positive y value in the x-y plane. The new frame of reference is only established when all three reference markers have been selected. After this, picking any one new reference marker will immediately establish a new frame of reference. Changing the orientation causes a rotation about the currently defined origin which will remain at 0,0,0. If one of these reference markers is moved to a new location in the data space, the user frame of reference will change while the marker is moving.
The user position can be separately defined at any one marker, either by setting the origin (x=0;y=0,z=0) at the chosen marker or by setting user defined values at the marker. This shifts the frame of reference without any rotation of the axes.
The user can also define the sense of the z-axis by flipping values in this axis. This will flip about z=0 so if the set XYZ at Marker option is used, care should be taken to ensure that the intended frame of reference is established.
The Align View button rotates the view of the data set so that the user defined frame of reference is rotationally aligned with the screen frame of reference. The X-axis is horizontal with negative values to the left. The Y-axis is vertical with negative values at the top. The Z-axis is out of the screen with negative values at the back (unless Flip z-axis has been used to invert the z-axis). The origin is not shifted to the centre of screen.