An overlay is a set of values for vertices displayed on top of the surface with a color scale. It is normally used as a functional activation overlay, but can really be any floating point value per voxel.
The source data can be a .w file, which is a file of scalar values associated with vertex indices. This data is associated by vertex index, so needs no additional registration. It's just painted right onto the surface, which is why it's sometimes called a paint file.
The source data can also be a volume. In this case, the surface is intersected with the volume in real space, so the volume needs to be registered to the surface somehow. Volumes can have more than one frame of data, which translates into time points. Additionally, some volume types have header data which describe how additional frames should be interpreted as time points or conditions, such as output from the fsfast stream.
TkSurfer can load up to eight overlays, although it can only display one overlay layer at a time.
Loading Overlay Files
To load an overlay file, use the File->Load Overlay... item or control-right click the overlay button in the toolbar. You will be prompted for the overlay file name and the layer in which to load the file. Specify a .w file (deprecated) or a .mgh volume file. If you specify a volume, you must also choose a registration method (if you are loading a .w file, ignore the 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 volume, 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. Note that an orig volume must be present for the subject you are loading for this method to work.
Overlay File Display Options
To select which overlay to show, use the View->Overlay Layer submenu or click the * button to the right of the overlay label in the information area of the tools window. The field names are automatically set to the file name loaded. You can change this name by typing a new one into the information area in the Tool window.
The display for the current overlay can be configured in the View->Configure->Configure Overlay Display dialog. Here are the options:
Opacity: This is the opacity of the overlay data.
Location: If the data you have loaded has multiple time points or conditions, you can select which one to show with the Time Point and Condition fields.
Color scale: This simply chooses a color scale with which to display the data. Curvature usually uses green/red, functional data usually uses heat scale, and field sign data usually uses blue/red.
Truncate: If checked, this will turn off the display of negative values.
Inverse: If checked, this will reverse the sign of the values as they are drawn in the color scale.
Complex: If checked, interprets the data as complex values.
Ignore Zeroes in Histogram: If checked, zero values will not be shown in the histogram. If the overlay is sparse and has few non-zero values, this can save a tall spike of zero values in the histogram that makes it hard to see other 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. You can configure the thresholds either by entering values into the labeled fields, or by clicking on the histogram. To set using the histogram, click with the left button to set the Min threshold, the middle button for the Mid threshold, and the right button for the Max threshold. When you click the Apply button, the colors of the value bars in the histogram will change to reflect the new color scale. Note how the threshold bars on both the positive and negative sides of the histogram update.
The Offset field, primarily, shifts the axis to the offset value horizontally. After you enter a non-zero offset in the textbox, all actions pertaining to the histogram from thereon are relative to the offset. The lines are now symmetric to offset value rather than 0 point. The Min, (Mid) and Max text entry boxes show values which are relative to the offset and the values you enter in the boxes are relative as well. To get back to normal settings, enter 0.0 in the Offset field.
Copy Settings to Layer: Choose a layer and click this button to copy the layer settings to another layer.
Apply changes to all layers: If this is checked, clicking Apply will apply your changes to all layers, changing the settings of all layers to the current values.
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 Only Marked checkbox is checked, only values that are marked will be considered.
Click the Apply button to see your changes.
NOTE: If you are finding that the "Configure Overlay Display" dialog is being clipped, where it becomes impossible to see or interact with the buttons below a certain point, this has been found to happen with low-resolution monitors. For an example, click here to see a screenshot (Thanks to Gonzalo Rojas Costa). To fix this (only for FS v5.1.0), copy the file available here to your $FREESURFER_HOME/lib/tcl directory. With this fix applied, the new dialog should look like this.
Saving Overlay Files
An overlay should be written out to a .mgh file; binary volumes cannot be written from overlays. To write a .mgh file, choose File->Save Overlay As..., and choose a file name and layer from the dialog box.