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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.

Method reference ('glm.Help('SingleStudy_tMap')')

  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

Reference notes

The .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.

Usage example

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:

  • instruction
  • motion in left visual field
  • motion in right visual field
  • motion in both visual fields (at the same time)
  • static (trials without any motion)

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
% clean up

Usage notes

Please note the following details about this method and the example:

  • at this time, the name of the contrast(s) cannot be specified but has to be set after the call
  • multiple contrasts can be given whereas the number of contrasts is the number of columns in the weights argument
  • each contrast should either have its weights be all positive (or all negative, weighted contrast over baseline, or reversed) or sum up to 0 (weighted differential contrast between conditions); in other words, contrasts with weights of different sign where the weights do not sum up to 0 are invalid for direct hypothesis testing!
glm.singlestudy_tmap.txt · Last modified: 2010/08/24 13:39 by jochen