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Time Course

The Time Course is a binary volume with multiple time points or conditions. The data is displayed in a graph so that all time points can be seen for a given vertex. When a vertex is clicked, the corresponding voxel is found in the binary volume. TkSurfer graphs the data for all time points at the chosen vertex.

Loading Time Course Volumes Loading binary volume Overlays and Time Course data is similar. Use the File->Load Time Course... command to load a time course volume. TkSurfer requires functional volumes to be in binary volume format. It will look for a header file with the same stem as the slice data or just guess the dimensions from the bfile. You need to specify the directory of the data, the stem, and optionally, a registration file. The format of a bfile name looks like this:

/path/to/data/stem_000.bfloat BR /path/to/data/stem_000.bshort

The numbers go from 0 to the number of slices minus one. The 'stem' represents any text that appears before the underscore before the number in the bfile.

You can specify a registration file to use. If you do not, TkSurferwill look in the same directory as the bfile data for a file called register.dat. A registration file is a matrix that defines the translation between anatomical RAS space and functional RAS space. TkSurfer uses this to align the functional volume with the anatomical volume.

The Time Course is displayed in a separate graph window. The graph will only be shown if the Time Course volume has more than one time point. Clicking on a vertex in the Display Window finds the corresponding functional voxel based on the registration and displays the values at that voxel for all time points in the graph window.

If there are multiple conditions defined in the header file, each condition will show up as a separate line in the graph. The legend on the right side of the graph window displays what line corresponds to what condition. By moving the mouse over a condition label in the legend, the corresponding line in the graph will be highlighted. This is useful for picking out one condition in a crowded graph.

You can also zoom into the graph. Click and drag with button 2 to draw a box around the area of interest. The graph will be resized around that box. Click with button 3 to zoom back out.

You can specify an average area to graph in two ways. You can click the vertices you want, marking them, and then choose Tools->Graph Marked Vertices Avg to graph the average. (Note that loading a patch marks vertices, so you can also graph the average of a path this way.) You can also load a label and graph the average of it with the Tools->Graph Label Avg.

The contents of the graph window can be written to a Postscript file with the Tools->Save Graph to Postscript File... command. It can then be included in another document or printed.