Brainload Command Line Tools

Brainload comes with some command line tools which demonstrate example usage of the library and make some of its the functionality available to non-programmers.

Available command line tools

  • brain_vol_info: Query voxel values from a volume file, e.g., a structural scan in MGH or MGZ format like mri/brain.mgz.

  • brain_morph_info: Query the values from a morphometry file like surf/lh.thickness.

  • brain_mesh_info: Query vertex coordinates and faces from a surface file like surf/lh.white.

  • visualize_verts: Visualize brain surface vertices. Generate a text file overlay that can be read by freeview that colors the given vertices.

  • brain_qa: Tool to check the consistency and availability of pre-processed FreeSurfer data for a study. Checks whether all requested data files are available for all subjects, and whether the data are consistent.

Getting help on command line tools

All command line tools come with detailed built-in help. Run them with -h or --help to access it. Example:

brain_vol_info --help