Turbo-BrainVoyager v4.4

Contrast Definition Files

While contrasts may be auto-generated by TBV, a Contrast Definition file (file extension ".CTR") allows for full control over the definition, names and colors of contrasts. The contrast file is used by TBV if selected in the "ContrastFile" entry in the "Statistics" tab of the TBV settings file. Alternatively, you may edit the respective entry directly in the settings file.

A contrast definition file (version 3) starts with a series of entries (see below). The most important general settings are "NrOfContrasts" specifying the number of defined contrasts and "NrOfValues" specifying the number of entries per contrast. This value must match the number of conditions in the used stimulation protocol if the "BaselineInContrasts" entry is set to "1" and if the protocol contains a baseline condition. If the "BaselineInContrasts" entry is set to "1" (recommended), the contrasts must contain an entry for the baseline at the first position (internally the baseline condition is not explicitly modeled in the design matrix, this is only relevant for display). In the context of automatic generation of contrasts it is strictly necessary that a baseline condition is contained in the protocol, which must be defined before other conditions (i.e. at position 1). When specifying contrasts with a contrast file, the "BaselinePosInProtocol" entry may be used to specify which condition corresponds to the baseline condition. By setting this value to "0", it is even possible to use protocols that do not contain an explicit baseline condition (this is often the case in event-related designs).

After these "header" definitions, four sections describe individual contrasts in detail. The "ContrastNames" section defines the names of the contrasts (here 3). The names may be any string and must be enclosed in quote signs ("); they appear as specified in the Contrast Window. The names in the example contain both the actual vector definition (see below) as well as with actual condition names. The actual definition of the contrast vectors used for internal calculations follows in the "ContrastVectors" section. Each row corresponds to one contrast. In our example (see below), the baseline condition appears in the contrasts at the first position (e.g., "-1" in the first two contrasts and "0" in the third contrast). The two first contrasts below actually test for the significance of individual beta values of the model (b_Faces, b_Houses) since the baseline condition is not explicitly modeled, while the last contrast compares the beta values of the two main conditions, "Faces" and "Houses". The next section determines whether a contrast is selected initially or not. A value of "0" indicates that the respective contrast should not be shown when starting real-time analysis; it can be, however enabled any time by clicking in the Contrast Window. A value of "1" indicates that the contrast is enabled in a one-sided manner, i.e. only positive t values surpassing the threshold will be shown (">" contrast). A value of "2" indicates that the contrast is enabled one-sided showing only negative t values surpassing the theshold ("<" contrast). A value of "3" indicates a two-sided contrast, i.e.voxels surpassing either the positive or negative threshold will be shown. The last section ("ContrastColors") contains the definition of the colors of the contrasts in RGB values. In the example, the first contrast is colored in red and the second in green matching the respective colors of the protocol; the third contrast, comparing the two main conditions, is colored in blue.

Here is an example of a contrast definition file for a protocol with one baseline and two main conditions:

<---------- FFA_PPA.ctr ---------->
FileVersion:           3
NrOfContrasts:         3
NrOfValues:            3
BaselineInContrasts:   1
BaselinePosInProtocol: 1
ContrastNames:
"[-1 +1  0] Faces vs. Baseline"
"[-1  0 +1] Houses vs. Baseline"
"[ 0 -1 +1] Houses vs. Faces"
ContrastVectors:
 -1  1  0
 -1  0  1
  0 -1  1
InitialSelectionState:
0
1
3
ContrastColors:
 255 0 0
 0 255 0
 0 0 255
<---------- FFA_PPA.ctr ---------->