Functional Volumes

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 Data

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 specify a registration file to use. If you do not, TkMedit will 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. TkMedit uses this to align the functional volume with the anatomical volume.

The Time Course volume can also have an offset volume. This must be specified from the command line. See the reference section for details.

Overlay

Display Options

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.

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.

Ignore threshold: Check to display all the values in the volume with a linear threshold, disabling the threshold values.

Threshold minimum / midpoint / slope: Configures the heat scale display. The minimum is the lowest value shown. The maximum is defined by ( (1/slope) + midpoint ).

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.

Registration

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, fMRI, 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 MGH-NMR 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.

Time Course

Graph

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.

Display Options

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, condition 0 is hidden. 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.