We renamed the output files from ANTs because Mindboggle requires two things: file names need "ants" in the prefix;  and 2) file names of the segmentation posteriors must be numbered with a two digit number (e.g. 02 rather than 2). 
We loaded the virtual environment that the Mindboggle authors designed, using the program Singularity by mapping our directory to the Mindboggle's home directory. Once in Mindboggles' home directory input the T1 image, and for Freesurfer, give the participant ID number. The plugins and number of threads identify the resources necessary to do the processing on the compute nodes on the BYU Fulton Supercomputer. The final line of code indicates the path to the output directory. Output formats include NifTi format for volume files, VTK format for surface meshes, and comma-dilimited (CSV) format for tables. Integers in each file correspond to anatomical labels or features.  Data are output in the original subject's space.