Cortical Surface Guided Tracing  


1. Use the Simple Brain Extract to Create a Brain Surface

See here for step-by-step examples of creating brain segmentation and surface.
After segmentation and surface creation you should have a cortical surface and brain labels:
(Save the surface now so you can return to it later in rview.)

cst1

2. Clear Segmentation

Use the replace label function to remove any brain volume labels and clear the segmentation ready for region tracing:
(note: the surface you have created is stored separately from the manual label data... it should also be saved separately)

cst2
(Note: labels and surface colouring are cleared)

3. Capture the Approximate Intensity Range of the Gyri of Interest:

Use the draw and fill mode with the intensity range reset to select voxels n one of the planes.
See Here for a more detailed description of selecting tracing intensities.
Note: be careful to select both grey and white matter but not CSF!

cst3


Capture range of intensities from Labelled Region:

csf4

4. Start tracing regions:

Start tracing regions using the Draw and Fill Mode of the segmentation tool:


cst6


Notes:

The labels being traced below the current surface are shown on the surface view together with the slice views.
(You may want to switch between low and high res rendering to vary the speed/quality of the rendered update depending on the speed of your machine: See the rendering tool for more details)

You can switch between the different slice and rendered views at any time using the segtool display layout buttons

Use the Zoom keys to zoom into the area of interest.

Use Current Label control to vary the label when marking different gyral structures