Connectivity Toolbox

The conn Functional Connectivity toolbox is a MATLAB-based program that hijacks SPM to do some data de-noising and remove potential artefacts that might skew your connectivity data. It is somewhat geared towards voxel-space analyses, but can support the surface-space analyses that we typically do in our lab. The walkthrough below is geared towards running conn on your FreeSurfer data.

Preconditions

These instructions assume that you have functional and anatomical data organized in the manner that FreeSurfer expects, and that you have completed the autorecon steps on the T1 anatomical file and have generated the surface meshes for your target participants. These instructions will also assume that you have dropped some number of initial volumes from the BOLD runs (usually the first 4) if required. If working from the raw data archived from the CTRC scanner, this will be a required step; if you are working with BOLD data that has already been analyzed, or preprocessed this may already have been done, and you will not want to drop yet another initial 4 volumes!

Because conn runs on top of SPM, you need to ensure that SPM is in your MATLAB path. Of course, conn also needs to be in your path. Check that they are using the which command in the MATLAB command window:

>> which spm
/opt/spm12/spm.m
>> which conn
/opt/conn/conn.m

If you see the paths to both .m files, you can run conn from the MATLAB command window:

>> conn