Fast manual lesion segmentation in ITKsnap

When finished, save the newly drawn image with "Segmentation" - "Save Segmentation Image".
This is a video-tutorial showing the basics of drawing brain lesions in ITKsnap. The interpolate tool allows the user to draw the lesion every few slices, and then interpolate the drawings to create a full lesion. Obviously, this method serves well if the lesion forms just one 3D shape. If the lesion for your patient forms more than one 3D shape, you can interpolate one part, and draw the other slice by slice. You can also label the different parts with different values, and interpolate each of them separately (i.e., first Label 1, then Label 2). In this case you would need to merge the labels in another software (thresholdImage in ANTs, or some c3d command).