CONN's GLM module runs General Linear Model group-level analyses of arbitrary user-defined data sources.  Data sources may include 3D-volume, 3D-surface, or 2D-matrix NIFTI files, containing arbitrary values/measures at each voxel/element ( e.g. task-activation responses, volumetric measures, DTI-based anatomical connectivity measures, etc.). The GLM module provides simple access to all inferential methods available in CONN, including parametric cluster statistics (SPM Random Field Theory), non-parametric randomization/permutation analyses, Threshold Free Cluster Enhancement analyses, etc. 

The GLM module can be used interactively using the Matlab syntax:

>> conn_module GLM

(note: if using CONN standalone version, use the OS command "conn module ###" in place of any Matlab command of the form "conn_module ###")

or programmatically, by first defining the group-level analysis details in a simple .cfg file like the following:

















1 1 1 1 1 1 1 0 0 0 0 0 0

0 0 0 0 0 0 0 1 1 1 1 1 1


-1 1



example group-analysis .cfg file (see group-analysis .cfg documentation for additional details of this file format) 

and then running those analyses using the syntax:

>> conn_module GLM /data/config_analysis01.cfg

The results of the second-level analyses will be stored in the directory specified in the #folder field. The contents of this directory are the standard SPM analysis outputs, including an SPM.mat file containing the details of the estimated General Linear Model and which can be loaded in SPM, beta_*.nii files containing maps of estimated effect-sizes for each model regressor, as well as con_*.nii and spmT_*.nii or spmF_*.nii files containing maps of estimated contrast values and T- or F- statistics.  

example contents of second-level GLM results

Last, group-level analysis results can be displayed using the syntax:

>> conn_display /data/analysis01

example output display of group-level analysis; see CONN DISPLAY for additional details