Functional data can be viewed in TkMedit as an overlay onto the anatomical data (or any other volumetric data) or in a graph, as in a time course. TkMedit can hold one volume for each purpose in memory at the same time. The volumes can be the same, i.e. a volume can be viewed as an overlay and as a time course, or separate.
Loading Overlay and Time Course data is similar. Use the File->Load Overlay Data... or File->Load Time Course Data... command to load in a functional volume. You can also control-right click the Overlay button on the toolbar to bring up the load dialog box.
You must specify a registration method to use. This determines how the functional volume will be registered onto the Main anatomical volume. 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 wish to register the functional volume, use this option. It will calculate a proper "identity" matrix based on the parameters of the functional and anatomical volumes.
The Time Course volume can also have an offset volume. This must be specified from the command line. See the reference section for details.
The Overlay is displayed, as implied in its name, as a translucent overlay in the Display Window. Its default state uses a heat color scale, in which negative values are drawn in blue and positive values are drawn in red. A threshold is used to limit the values shown and define a color ramp so that more values close to the maximum or negative maximum or red or blue and values close to the minimum or negative minimum are yellow or teal.
The Overlay display can be turned off by unchecking the View->Functional Overlay option. Other aspects of the Overlay display are configured in the dialog box available in View->Configure...->Functional Overlay.... The following options are shown:
Time Point / Condition: Changes the currently shown time point or condition in the Display Window. The range is shown in parentheses next to the label. Note that a header file must be present in order to specify the division of data between time points in conditions, otherwise TkMedit assumes multiple time points and no conditions. Additionally, you may play a 'movie' of time points using the play and stop buttons. The play button has the symbol |> and the stop button has the symbol . Truncate negative / positive values: Check to turn off the display of negative or positive values. Reverse values: Check to display negative values in red and positive values in blue. Grayscale: Check to use a grayscale color scale instead of the normal blue to red heat color scale. The lowest, most negative values will be shown in black and the highest, most positive values in white. Opaque: Check to make the Overlay opaque. If unchecked, values below the min and above the -min will be transparent. If checked, they will be drawn in black. Sample Type: This may be Nearest Neighbor, which will draw all the voxels without interpolation, or Trilinear, which will do some blending of the voxels for a smoother display. Ignore threshold: Check to display all the values in the volume with a linear threshold, disabling the threshold values. Threshold type: In Linear mode, the color map is a linear scale from min to max (see below). Values below min will not be displayed, the value of min will be dark red, the value of max will be yellow, and all values above max will be yellow. In Piecewise mode, two linear scales are used: one from min to mid, and another from mid to max. You can also set the second linear scale using a slope instead of specifying a max. Threshold minimum / midpoint / maximum / slope: Use these values to set up the linear or piecewise threshold scale. To set the values, enter a value in a field, and press return. Then click the Apply button to use the new scale. When setting the max or slope, pressing return when setting one value will update the other value accordingly. Overlay Alpha: This controls the translucency of the overlay. Set Threshold Using FDR: This will automatically set the threshold values using False Rate Discovery. Enter the rate in the field next to the button. If the Mask to Brain checkbox is checked, only values that fall within the brain volume will be considered. Note that if the Mask to Brain checkbox is checked, there must be a volume titled brain in the subject's mri directory. This volume will be loaded on the fly as a mask.
Note that the Apply button must be clicked for changes to take effect.
The View->Mask to Functional Overlay option is available to only draw areas of the anatomical volume that are in the valid space of the Overlay volume. This gives you a better sense of the entire Overlay volume and how it relates to the anatomical volume.
If you have an Aux volume loaded, you can use the View->Make Functional Overlay to Aux Volume option to mask the overlay to non-zero values in the Aux volume. This is useful if you want to mask the overlay to the brain volume. Just load the brain volume in as the Aux volume, and activate this option.
The View->Functional Color Scale Bar, active by default, draws a color bar on the right side of the Display window that can be used as a key to match color intensities to value. Note that functional values will also appear in the bottom of the Tools window. The color bar is mainly useful for screen shots. This can also be turned on and off by the toolbar button.
If enabled, you can use TkMedit to register the Overlay volume, or align the Overlay volume with the anatomical data. This changes the registration file. Use the Tools->Register Functional Overlay command to bring up a dialog box containing arrow buttons. Use these buttons along with the associated parameters to move the Overlay volume.
You can save your changes to the registration file with the File->Save Overlay Registration item. You can restore the registration to its original state with the Tools->fMRI->Restore Overlay Registration. Use the Tools->fMRI->Set Registration to Identity command to set the registration matrix to the identity matrix.
Note that since registration can affect the validity of any data analysis you perform, the processing stream only allows registration at a specific point in the stream. Registration may not be available at all times. It can be enabled from the command line at start-up time. See the reference section for details.
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 voxel 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.
If the same volume is being used for the Overlay and the Time Course, clicking in the graph window will change the time point in the Overlay display to what x point was clicked. You can use this method to navigate the Overlay volume.
The selection / label can be used to specify an average area to graph. To graph a selection / label as an average, draw or load a selection and choose Tools->fMRI->Graph Current Selection. The title at the top of the graph will change to show that a selection is being graphed instead of a single voxel. The contents of a selection can be printed to a text file in a chart form with the Tools->fMRI->Print Time Course Summary to File... command. You can use this data in a separate graphic program.
The contents of the graph window can be written to a Postscript file with the Tools->fMRI->Save Time Course Graph to Postscript File... command. It can then be included in another document or printed.
The graph can be configured with the View->Configure...->Time Course Graph 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:
Show error bars: If this box is checked and error data is present, vertical errors bars will be drawn at each data point, signifying the possible error for each value. Automatically size graph: If checked, the graph axes will automatically resize according to the range of values. If unchecked, the axes will stay static. Subtract pre-stim average: If checked, the average value of the values before the stimulus (time second = 0) for each condition is subtracted from all values. This effectively adjusts the y axis to normalize for pre-stim values. Show percent change: If an offset volume is available, this will show the percent change for each value instead of the raw value itself. Number of pre-stim points: Originally defined by the header file, this value lets you adjust the time = 0 value. Time resolution: This is defined by the header file and is used to calculate how many seconds are in each time point.
Note that the Apply button must be clicked for changes to take effect.