Getting MNI coordinates of Probe Projection to Cortex - BUNPC/AtlasViewer GitHub Wiki

Once the probe geometry has been created and positioned on the atlas head, it should be evaluated to determine if it is successfully targeting the desired brain regions.

After a probe has been registered to the surface, check the “Hide Springs”, “Hide Dummy Opts”, and “Show srcs/dets” in the Probe box, then go into the Tools menu --> Project Probe To Cortex --> Project, as shown below.



Click the “Curr Subject Optodes” in the pop-up window. The vectors perpendicular to the surface at the optodes will then appear. The location where each of these vectors meets the cortical surface will then appear in a popup window, shown in the following figures.







Similarly, clicking the “Curr Subject Channels” in the pop-up window will draw a vector perpendicular to the surface at the midpoint of each SD pair, and get the table containing the channel coordinates in the Monte Carlo space, channel position in the standard MNI coordinate space, and a label assignment for the corresponding brain region defined by the “Automated Anatomical Labeling” (AAL) in https://doi.org/10.1006/nimg.2001.0978.







The values in this table can be easily copied into your own text file or spread sheet for further analyses. The details of this labeling procedure are provided in 10.1016/j.neuroimage.2006.10.043 and https://doi.org/10.1016/j.neures.2011.10.008.

Knowledge of these standard MNI coordinates and the corresponding cortical label enables the user to compare their results for given channels of data against other fNIRS and fMRI studies reporting results using the same standard MNI coordinates.

By clicking the “Display MNI Projection” button and entering the MNI coordinates in the pop-up window, the user can visualize the Automated Anatomical Labeling on the surface of the brain in order to visualize the location of each channel with respect to the labeling.



By clicking the “Labels” radio button under the “Brain Display” panel, the colormap for the anatomical labeling can be changed to a variety of options using the menu item “Tool → Choose Labels Colormap,” as shown below.



Note that all of the work performed in registering the probe and obtaining the cortical projections can be saved at any time with the menu item “File → Save Viewer State.” This will save the current state of AtlasViewer in the file atlasViewer.mat in the subject root folder. When AtlasViewer is launched again in this directory, it will read this file and return AtlasViewer to the same state.