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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.

The source data is a volume. The surface is intersected with the volume in real space, so the volume needs to be registered to the surface somehow. Only some volume types (namely the binary volume type, .bshort or .float) have header data which describe how additional frames should be interpreted as time points or conditions. Some can have multiple frames but don't break them into conditions, so they are just interpreted as time points in the same condition. TkSurfer will do its best to guess the proper format for you.

Loading Time Course Volumes

Loading 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 a volume format; the .w format is not support. You must specify a registration type. These are the options:

Specify registration file

If you have a register.dat file, probably generated by TkRegister, use this option to specify it. The file contains a transformation matrix, some information about voxel size, and a rounding method.

Find registration in data directory

If you have a register.dat file in the same directory as the data file, use this option to automatically look in that directory.

Calculate identity matrix

If the functional volume is in the same alignment as the anatomical, or you do not with to register the functional volume, use this option. It will calculate a proper "identity" matrix based on the paramters of the functional and anatomical volumes. Note that an orig volume must be present for the subject you are loading for this method to work.

Graph Window

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->Time Course->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->Time Course->Graph Avg Label.

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

Display Options

The graph can be configured with the View->Configure...->Time Course... dialog box. The top part of this dialog is a list of mappings between colors and conditions. You will see as many rows as the Time Course volume has conditions. You can assign a color to each condition with the number field on the right or hide colors / conditions with the checkbox on the left. By default, if there is more than one condition, condition 0 is hidden. This is for compatibility with some of the data that the FsFast stream creates. You can also enter a name for the color in the column on the left. This name will show up in the graph window in the legend on the right.

The bottom part has the following options:

Note that the Apply button must be clicked for changes to take effect.