GLM

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:

config_analysis01.cfg

#data

/data/beta_sub01.nii

/data/beta_sub02.nii

/data/beta_sub03.nii

/data/beta_sub04.nii

/data/beta_sub05.nii

/data/beta_sub06.nii

/data/beta_sub07.nii

/data/beta_sub08.nii

/data/beta_sub09.nii

/data/beta_sub10.nii

/data/beta_sub11.nii

/data/beta_sub12.nii

/data/beta_sub13.nii

#design

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

#contrast_between

-1 1

#folder

/data/analysis01

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