When MRI data are available for an fNIRS subject, their structural data may be imported into AtlasViewer after it has been processed by FreeSurfer30,31 and separated into surfaces using the “write_surf.m” script to save the pial mesh. It is assumed that the user already has very good surfaces created using FreeSurfer before beginning this process. Surfaces of the brain and head can be created by others means, of which there are many such methods available, but the results need to be saved in FreeSurfer format using the write_surf.m script provided with AtlasViewer. The following two files are required, “headsurf.mesh” and “pialsurf.mesh,” and they should be in the “anatomical” subdirectory of the subject folder. Once these two files have been prepared, the user can use the MATLAB® script “create_HeadVox.m” (available at 32) for producing the several additional files needed to use a user supplied anatomy in AtlasViewer. Briefly, the process is to run the script “create_HeadVox.m” to generate the files “headvol.vox,” “headvol_dims.txt,” “headvol_tiss_type.txt,” “headvol_dims.txt,” “headsurf2vol.txt,” “pialsurf2vol.txt,” and “refpts2vol.txt.” All of these files are saved in the “anatomical” subfolder of the subject directory. The file “headvol.vox” is a 3-D volume of voxels designating the head and pial surfaces. The labels used are “0” for air, “1” for extracerebral tissue between the head and pial surfaces, and “2” for brain tissue inside the pial surface. The differentiation between these volumes is critical for visualization (Fig. 1), probe registration to the scalp (Fig. 4), and photon migration in the Monte Carlo random walk (Sec. 4.1), upon which all image analysis is dependent. Once these files are created and saved in the “anatomical” subfolder, the user can then load the subject-specific anatomy by running AtlasViewer. The last step is to define the 10-20 scalp reference points. This is accomplished via the menu item “Tool → Find Ref Points,” which will open a new window that allows the user to select and save the five anchor reference points Nz, Iz, A1, A2, and Cz. Once these are saved, the user should then use the menu item “Tool → Recalculate 10-20 pts” to generate the positions of all 10-20 reference points.5 At this point, all of the AtlasViewer features described above can be used on this user supplied head anatomy.