Getting Started

Loading the CONN Module

The SCC uses a module system to load and access software packages. Refer to our module page for more extensive documentation.

To see all versions of CONN available on the SCC:

[scc4]$ module avail conn

--------------------------- /share/module.8/imaging ----------------------------
   conn/17.f    conn/18.b    conn/21.a    conn/22.a    conn/22v2407 (D)    conn/25b

  Where:
   D:  Default Module

Note that conn/22v2407 is the default — the version you get if you do not name one — and that it is not the newest build. Pin an explicit version so your analyses stay reproducible.

CONN Needs MATLAB and SPM

Unlike the other imaging tools documented here, CONN is not a self-contained program. It is a MATLAB toolbox that sits on top of SPM, so three modules must be loaded, in this order:

[scc4]$ module load matlab/2024b
[scc4]$ module load spm/25.01.02
[scc4]$ module load conn/25b

Load them out of order, or load conn on its own, and the module system refuses with an error naming the modules you still need and the order to put them in. Follow what it tells you.

Each CONN version pins its own MATLAB and SPM versions, so the chain is different for each:

CONN	SPM	MATLAB
25b	25.01.02	2024b
22v2407 (D)	12.7771	2023a

CONN 25b requires SPM 25 — SPM 12 is no longer supported.

Confirm the modules are loaded:

[scc4]$ module list

Currently Loaded Modules:
  1) matlab/2024b   2) spm/25.01.02   3) conn/25b

There is no conn command on your PATH. The module adds CONN to MATLAB's search path instead, so you start it from inside MATLAB — see Launching CONN.