Registering Atlas to Digital Points - BUNPC/AtlasViewer GitHub Wiki

As head size can vary across subjects, it is important to consider whether or not different head sizes will change the cortical regions sampled by the probe geometry. In the above manuals, we described designing a probe and registering it to the surface of an atlas head model. Instead, the atlas can first be registered to a specific head size prior to registering the probe design to the surface of the atlas. This allows the user to determine whether changing the head size causes a significant variation in the cortical regions sampled by the probe geometry.
The atlas can be registered to a specific head size using the menu item “Tool → Register Atlas to Head Size.”



This will cause a dialog box (see the following figure) to open up and ask for head circumference, distance from nasion (Nz) to inion (Iz), and distance from left auricular (A1) to right auricular (A2) as measured along the scalp surface of the subject using a tape measure in centimeter units. AtlasViewer is also able to automatically read in head size data in the subject folder where it finds a file named "headsize.txt". More information could be found from here.



This tool will then calculate an ellipsoid that matches these dimensions to establish the coordinates of 10-20 reference points Iz, Nz, vertex or central zero (Cz), A1, and A2. The atlas is then registered to these five 10-20 reference points using an affine transformation.

BUT this approach can be problematic because of the challenge in accurately measuring the distances and because it assumes an ellipsoid shape for the head. Alternatively, more accurate registration of the atlas to the subject can be achieved using a three-dimensional (3-D) digitization system. In this case, the user can import measurements of the coordinates of these five 10-20 reference points on a given subject. AtlasViewer requires these coordinates to be specified in a digpts.txt file. An example of the text file is shown in the following figure.



In this sample digpts.txt file, the first five lines are required and define the positions of the five key reference points to determine the affine transformation from the atlas space to the digitized space of the subject. In the following lines, sources and detectors are defined in the same 3-D space as the reference points and are identified as s1, s2, and so on for sources and d1, d2, etc. for detectors.

If a correctly formatted text file, named digpts.txt, exists in the root subject folder then the menu item “Tool → Register Atlas to Dig Points” will be available. This function will register the atlas to the five reference points Iz, Nz, Cz, A1, and A2 using an affine transformation.



After clicking the “Register Atlas to Dig Points”, the atlas to the 10-20 reference points in digpts.txt will be registered, and AtlasViewer will display the positions of these sources and detectors on the registered atlas without the user having to add springs and anchor points to their probe design.

As shown in the figure below, the source and detector optode positions are visible on the surface of the head. Showing sources and detectors versus optodes is achieved with the “Show srcs/dets” check box. AtlasViewer will utilize the imported SD file to obtain the measurement list that defines all pairs of sources and detectors used for measurements. These measurement channels can also be visualized on the head surface by unchecking the “Hide Meas List.”