Documentation
Technical documentation
Whitfield-Gabrieli, S., & Nieto-Castanon, A. (2012). Conn: A functional connectivity toolbox for correlated and anticorrelated brain networks. Brain connectivity, 2(3), 125-141
Nieto-Castanon, A. (2020). Handbook of functional connectivity Magnetic Resonance Imaging methods in CONN. Boston, MA: Hilbert Press
Software documentation
General software use: CONN toolbox manual
Using CONN in the context of High Performance Computing clusters or multi-processor environments: CONN grid, Cluster configuration
Scripting
Main user-facing scripting functions in CONN:
>> conn_batch
create and manage all aspects of your functional connectivity projects using scripts
>> conn_module
integrate modular CONN functions into your own preprocessing or analysis pipelines (for arbitrary / non-connectivity data)
Other useful scripting commands in CONN
manages jobs submitted to cloud or HPC environments
>> conn submit run <filename.m>
submits arbitrary Matlab script <filename.m> as a single job to your cloud or HPC environment
>> conn submit_spmbatch <matlabbatch>
submits arbitrary SPM batch <matlabbatch> (.m or .mat file, or matlabbatch structure) as a single job to your cloud or HPC environment
>> conn module preprocessing <filename.json>
preprocesses and/or denoises arbitrary functional data
>> conn module glm <filename.json>
performs group-level analyses of arbitrary data (including analyses of standard 3D volume-level data, as well as surface- and matrix-level analyses)
displays group-level analysis results (including analyses of standard 3D volume-level data, as well as surface- and matrix-level analyses)
>> conn_surf_write
writes surface- level data (FreeSurfer fsaverage level-8 tessellation) into NIFTI format file
>> conn_mtx_write
writes matrix-level data (arbitrary square matrix) into NIFTI format file
Examples of use: see "How to..." sections in fMRI Methods