This process provides the user with flattened images of the whole brain or select parts (e.g. occipital lobe) of the brain.

Cutting the Full Surface

The full surface represents an entire hemisphere without the mid-brain (middle of the medial surface). First, load the subject surface into tksurfer:

tksurfer subjid lh inflated

Load the curvature through the File->Curvature->Load menu (load lh.curv). This should show a green/red curvature pattern. Red = sulci.

Right click before making a cut; this will clear previous points. This is needed because it will string together all the previous places you have clicked to make the cut.

  1. Make 5 relaxation cuts. For each cut, select the points (LEFT-CLICK) and then press the Cut icon (scissors with an open triangle for a line cut). Make the points fairly close together; if they are too far apart, the cut fails.
    • 1 cut down the calcarine (same cut as for the occiput surface)
    • 3 equally spaced radial cuts on the medial surface
    • 1 sagitally oriented cut around the temporal pole
  2. Encircle midline region (corpus callosum and mid-brain structures) to remove:
    • LEFT-CLICK sequence
  3. Make closed-line cut.
    • CUTAREA button
  4. Mark and fill region to save.
    • Single left-click in region to save.
    • Press Fill Uncut Area button (icon = filled triangle). This will fill the patch with white. The non-patch area will be unaccessible through the interface.
  5. Save patch.
    • Select File->Patch->SaveAs. Specify the patch name in the patch field.

    • The default names for the full cortical surfaces with the midline removed are:
      • rh.full.patch.3d
      • lh.full.patch.3d

Cutting the Occiput Surface

The occiput patch represents the occipital pole with a cut down the calcarine fissure. This cortical patch is particularly useful for displaying the results of visual experiments.

In tksurfer:

  1. Make calcarine sulcus relaxation cut.
    • Select points (left-click) along the calcarine fissure beginning at the occipital pole and moving anteriorly.
    • Open-line cut with CUTLINE (surfer tools).
  2. Specify cutting plane.
    • Select three points (labeled 1, 2, and 3 below) to define the cutting plane, and a fourth point (labeled 4 below) to specify which portion of the surface to keep (left-click).
  3. Make the planar cut.
    • CUTPLANE button.
    4.. Save patch.
    • Specify the patch name in the patch field and press WRITE.
    • ...
    • The default names for the occiput cortical surfaces are:
      • rh.occip.patch.3d
      • lh.occip.patch.3d