After running the regression for a single study (run, i.e. one FMR, VTC, or MTC object), creating t-contrast maps for just this study can be beneficial in determining whether or not a certain run contains too much noise (or specific artefacts) for it to be included in second-level statistics. Also, it is sometimes desired to use the actually standard-error-normalized effect-statistic (t instead of regression beta) for further computations (e.g. to incorporate a measure of within-subject-data noise on the second level).
You need to have a GLM file/object available that represents the regression outcome of a single run. Please note that, at this time, the support for FMR (MAP creation) has not been implemented; but as the MAP format lacks a lot of the properties (and thus flexibility) of the VMP format, it is also not suggested other than for very specific application, such as MVPA.
GLM::SingleStudy_tMap - calculate a t contrast map FORMAT: map = glm.SingleStudy_tMap([c, mapopts]) Input fields: c NxC contrast vector (default: full model and main eff) mapopts structure with optional fields .interp mesh-based interpolation (default: true) .srf surface file, required for interpolation Output fields: map MAP/VMP/SMP object with C maps
.interp option was intended to cover those cases where in (fairly “old” versions of BrainVoyager QX, 1.7.x), vertex nodes would sometimes lack an appropriate target when a Sphere-to-Sphere-Mapping (SSM) object had been specified. As this bug has been fixed (and a workaround is still available on the SMP side), this option will be removed in future versions.
Say you have a study with 5 regressors of interest and 1 confound (mean study level, automatically added by BrainVoyager QX/NeuroElf), whereas the conditions of interest are:
then the syntax to create a contrast over all conditions sharing motion in any visual field would be coded as:
% load a GLM (only needed if not yet loaded!) glm = xff('*.glm', 'Please select the single-study GLM...'); % create the contrast contrast = glm.SingleStudy_tMap([0;1;1;1;0]); % name the contrast contrast.Map.Name = 'Motion in any visual field'; % save the contrast contrast.SaveAs; % clean up contrast.ClearObject; glm.ClearObject;
Please note the following details about this method and the example: