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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:

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.

TkSurferGuide/TkSurferWorkingWithData/TkSurferOverlay (last edited 2011-06-27 12:06:31 by LouisVinke)