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

>> conn jobmanager

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)

>> conn display <SPM.mat>

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