Overlay

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 (namely the binary volume type, .bshort or .float) 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 five 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. You will be prompted for the overlay file name and the layer in which to load the file. Specify a .w file or a 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:

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. 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 choose 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.

  Reverse: ???

  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: The threshold configures how the overlay color map is calculated. All values below the Min and above the Max thresholds will be transparent. The Mid threshold is the midpoint of the color range. Note that this only configures half of the scale; the 'cold' part of the color scale applies to values from -Min to -Max, with -Mid being the middle. The slope value can be used to set the Max threshold based on the Min and Mid thresholds. You can configure the tresholds 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 Offest field is used to set a blue factor that will be added to the color values. All uncolored values will look blue, and red values will look less red.

  Copy Settings to Layer: Choose and layer and click this button to copy the layer settings to anothe 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.

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.