Overlay

An overlay is a set of values, 0 or 1 per vertex, displayed 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 volume can be a .w file, a file containing one value per vertex, previously registered with the volume. It can also be a binary volume or bfile. These are volumes of short integers (.bshort) or floating point values (.bfloat) with a corresponding registration file. Binary volumes can contain multiple time points and conditions.

Overlays can be loaded into any of five layers. TkSurfer can display one overlay layer at a time.

Loading Overlay Files

To load an overlay file, use the File->Load Overlay... item. You will be prompted for the overlay file name and the layer in which to load the file. Chose the .w file or a .bshort or .bfloat file if you are loading a binary volume.

If you are loading a binary volume, you will be prompted for the stem of the volume and a registration file. You may leave the registration file field blank if there is a registration file in the same directory as the binary volume named "register.dat."

Overlay File Display Options

To select which overlay to show, use the View->Overlay Layer submenu. 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. 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. You can select the color scale to use with the radio buttons in the top area of the dialog. The Truncate option can be checked to turn off the display of negative values. Check the Reverse option to reverse the sign of the values as they are drawn in the color scale. Inverse and Complex are reserved for future upgrades. Also see SettingTheOverlayColorScale.

Click the Apply button to see your changes.

Saving Overlay Files

An overlay can only be written out to a .w file; binary volumes cannot be written from overlays. To write a .w file, choose File->Save Overlay As..., and choose a file name and layer from the dialog box.