Marking and Using 3D Point Landmarks

Overview

Lists of 3D point landmarks can me manually entered and saved in RView: A set of landmarks is associated with each image volume (Reference, Float A, Float B etc...). Landmarks can be used both for recording locations in anatomy and manually quantifying alignment errors between images. Much of this tool is inspired by the registration tool (Xreg) developed by Derek Hill and Cliff Ruff at UMDS guys hospital in the early 1990's.

Landmark Tool

When an image set is loaded Landmarks can be entered by selecting the landmark tool from the Options->Tool menu:

This displays the landmark tool:

rview keeps track of multiple Point Lists, each can be associated with the coordinate system of a 3D data set

Reference image: List 0,
Floating image A: List1,
Floating image B: List 2

List Selection

The 'List #' control at the top of the landmark tool allows the current list being modified to be selected.

Point Selection

The 'Point #' control then allows the point within the list to be selected. If a list of points has been entered, modifying the point # for that list displays the co-ordinates of that point in mm in the list below, and allows the points to be stepped through in order. Stepping also displays the name given to the landmark (none by default). Typing text into the landmark name then modifies that landmark label, and moves the rview focus of the display to be at that point location in 3D space.

Entering New Landmarks

To enter a new point in a given list, select 'New Point'. When this is selected the cursor turns to a 'plus':

Clicking the RIGHT mouse button on any display plane then leaves a landmark at that point in the data space of that display plane:

As with normal viewing in rview, the LEFT mouse button allows the 3D focus of the slice displays to be changed. Landmarks are automatically given a text label equal to the numbering of their order of entry in that particular data set (here 1 landmarks has been entered and, since it has not been given a name, is simply labelled '#1'. Landmarks for different data sets are shown with different colours.
Note: Landmarks entered in the co-ordinate system of a floating image (A, B... etc.) are displayed using the current Alignment transformation for that data set.

Saving Landmarks

The sets of Landmarks selected in each data space may be saved to a text file using the 'Save List To File' Button

The locations of each point together with their label are all stored in mm co-ordinates. You can edit this file with a text editor to change the text labels or their locations, or import the files into a spreadsheet for numerical analysis. The format used is derived from that devised by Hill and Ruff in the Xreg X-windows based manual point registration software: Stating with a text label 'POINTLIST', followed by optional comment lines (beginning with a #), and then a list of the X, Y and Z mm coordinates of each point. The final columns are the weight factor (originally used by Xreg for manual alignment) and the text name. An example file is as follows:

POINTLIST # APointList # x y z weight name 72.000000, -46.500000, 0.000000 [1.000000] (none) 84.000000, 27.000000, 0.000000 [1.000000] (none) -54.000000, 6.000000, 0.000000 [1.000000] (none) -43.500000, -85.500000, 0.000000 [1.000000] (none)

Loading Point Landmarks:

Lists of points can be loaded to the appropriate dataset by simply dragging the point list file and dropping it into into the 'Reference' 'A', 'B' etc display plane.

Landmark Display Options:

Point Landmarks for each dataset are normally only shown i n the display plane for that data set. The Display Options for point Landmarks allow the setting of the display configuration to show all lists on all planes. They also allow the optional display of lines between neighbouring points:

The distance between the eyes!!!

Marking Landmarks on Surfaces

When ISO surface renderings are used, (See the Rendering tool), the landmark selection process will select point lying on the surface below the cursor (rather than the image plane as for slice displays)

Sets of lines and contours can then be drawn on the display, for example to trace sulci on the cortex:

surf1
Tracing a set of Landmarks along the Superior Temporal Sulcas

surfland2
Comparing Two Traces of Sulci.

surfland3
Using Cut Planes to view the depth of the traced Sulci

surflandmark4
Using cut Planes to place landmarks in the base of sulci

(Be careful when using rendered views only: Landmarks may not fall deep into sulci)

Evaluating Landmark Alignment Error

If you have marked two sets of homologous landmarks (i.e. point 0 in list 0 corresponds to point 0 in list 1) on the reference image and the floating image, rview will display the RMS error (in mm) between the locations of the sets of landmark pairs. To do this select the point list corresponding to the floating image landmarks you want the error from, and hit the 'RMS Error list 0->' button (i.e. RMS error from point list 0). This will display the error in the main info box:

rmsinfo

Note this error is the error between point lists, for the current rigid transformation between image spaces. i.e. the error between point list 0 and point list 1 is a function of the current transformation estimate between the reference image space and floating image A.

This provides a way of evaluating the automated transformation estimate with respect to landmarks selected in image pairs. However, landmarks should be selected carefully: They should be true 3D points and be in, or close, to the tissues of interest (particularly important when non-rigid deformation can occur between scans).

Clearing Point Lists:

To clear a set of points, Select the Point list to delete and then use the 'Delete List' button.