Brain Innovation

support portal

Random Effects Granger Causality Mapping

Authors: Rainer Goebel, Alard Roebroeck

The "RFX GCM" GUI plugin (version 2.5) operates as a wrapper to the single-subject GCM plugin; Consult the help of this core plugin for general documentation on running GCMs. This plugin allows to run several individual GCMs, one GCM for the data (one or more VTC files) of each subject. The produced main result consists of two volume maps, one for instantaneous Granger causality (INST maps) and one for directed influences (dGCM maps, i.e. difference GCM maps); each entry (row) in these two maps corresponds to the result from the data (one or more VTC files) of a single subject. The names of the resulting subject maps are prepared for running a "Combine VMPs" or "ANCOVA" random effects analysis that consists of a simple t-test (t > 0) in case of one group of subjects.

The RFX GCM plugin presents a tabbed dialog. The first Input Data tab is used to specify a VOI and a set of VTC files. If a VOI file is currently available, the file is loaded and the VOIs are listed automatically in the VOI list box; if no VOI file is available or if you want to use another VOI file, use the VOI file Browse ("...") button. If more than one VOI is referenced in the VOI file, the desired VOI need to be selected (you may rerun GCM analyses with a different VOI in a separate run of the plugin). In the standard mode, the program uses the same VOI as the reference region for all subjects. Better results are usually obtained if you have defined a specific version of a generic region-of-interest for each subject, e.g. by performing a functional localizer experiment. Such subject-specific VOIs allow to use different VOI coordinates for the corresponding (homologue) area across subjects (e.g. a (slightly) different "FFA" VOI definition for each subject). In this case, turn on the Use subject-specific VOIs option. The program expects that the subject-specific VOIs are defined by a combination of a "subject identifier" substring, followed by a "_" character followed by the respective VOI name. A seed region in the fusiform face area (FFA) of the right hemisphere could be named for subject 1, for example, as "Subj1_FFA-RH", for subject 2 "Subj2_FFA-RH" and so on. Note that in this mode a subject-specific VOI must exist for each included subject and that the subject ID must be identical for the VOI as well as for the VTC files belonging to that subject. In the example above, a VTC file for subject 2 should, thus, also start with the "Subj2_" substring.

The easiest way to add VTCs for multiple subjects is to use the Load From MDM button; since one usually runs also a multi-subject GLM, an appropriate MDM file is usually already available; alternatively, individual VTCs can be added using the + button below the VTC list box. All subject-specific GCM results (a ".gcm" and a ".log" file) are stored in the folder where the subject's (first) VTC file is located. The final results are two VMP files with the integrated "INST and "dGCM" data of all subjects (starting with the substrings "RFX_INST_..." and "RFX_dGCM..."); these files are stored in the folder where the loaded VMR file is located.

The second Epoch Selection tab is used to specify a condition name and the time windows of the VTCs that will be used to run GCMs. One RFX-GCM run will produce data for one condition; you may enter a name for the condition in the Condition name field; note that this name will appear in individual map files and final RFX volume map files in order to identify the content of produced files (together with the name of the selected VOI). A conditon name usually corresponds to the time windows representing the same experimental condition (e.g. "Faces" intervals). An easy way to select time windows is provided by the Use single interval per VTC method that simply uses the whole data from a VTC except for a specified number of volumes at the begin and end. This is a useful method to explore overall effective connectivity results across conditions or when a run reflects a single condition, e.g. resting state or viewing a movie. To specify specific condition-related intervals, select the Use protocol condition per VTC method. After selection of this approach, the protocol conditions list box is filled with the condition names extracted from the protocol attached to the first included VTC file. Note that for RFX GCM, each VTC file must have a linked protocol with the same conditions defined (but the same condition may have, of course, different interval specifications in different runs); the proper availability of all required information is verified when clicking the GO button.

After clicking GO, the plugin analyzes which runs belong to which subject using the initial substring of each VTC. The VTCs "S1_Run1.vtc" and "S1_Run2.vtc" would be assigned to belong to the same subject but the file "S4_Run1.vtc" would be assigned to another subject with the identifier "S4". If subject-specific VOIs are used, the program will also check that VOIs are defined starting with the same initial substrings as the VTC files. The results for the INST and dGCM maps are stored for each subject as a .gcm file (there will also be a ".log" file with additional information). The main output, however, are two VMP files, each containing all the data from all subjects with proper renaming of individual map names so that a "Combine VMPs" t test or ANCOVA t test can be directly launched subsequently.


At present, a RFX volume map can be created only for one condition. To compare two or more conditions, you can simply add the result of two (or more) multi-subject condition output maps using the Add VMP button in the Volume Maps dialog; The created multi-condition volume map can then be used as input for a one-within factor ANCOVA.

The GCMPlugin.ini file is used as described in the GCM Plugin help; The requested output maps listed in the "MapTypesComputed" entry are, however, ignored since the RFX GCM plugin always computes two maps, the "INST" and "dGCM" maps.