2D Surfaces

Scuba can displaye 2D intersections of 3D surfaces. This is most useful when overlaid onto a volume slice. You will see the cross section of the surface where it intersects the viewing plane.

Loading Surfaces

You can load a surface from the command line or from within the program. From the command line, use the -f option:

scuba -f FILENAME

If you have the SUBJECTS_DIR variable defined, you can use the -s option to declare a subject, and scuba will search for any file names passed to -f in the subject's surf/ directory. These are equivalent:

setenv SUBJECTS_DIR /home/myname/subjects
scuba -s bert -f lh.white

scuba -f /home/myname/subjects/bert/surf/lh.white

cd /home/myname/subjects/bert/surf
scuba -f lh.white

You can also pass in additional options to configure the layer that the surface will be displayed it, e.g.:

scuba -f lh.white:linewidth=3:linecolor=255,128,0

For example, this line sets the line width to 3 and the color of the line to pink. For additonal options you can pass in on the command line, see the scuba page for command line reference.

Alternatively, you can use the File->Load Surface... menu command from within the program to use a standard dialog box to load a surface. Note that this dialog box also has an option labeled, Automatically add new layer to all views. This is enabled by default. If checked, the layer that will display this surface will be added in the next empty slot to all existing views. This is probably what you want to happen, unless you specially want to exclude this surface from certain views.

Display Options

Like other layer types and data collections, display options for surfaces are in the Layers panel, and settings for transforms are in the Data panel.

In the Layers panel, you can configure the following things:

• Layer: This pull-down menu will let you select the layer to configure.

  Name: This editable field lets you change the name of the layer. Initially, the names of the layers are the same as the data collections they are drawing. You don't have to set or change the name, but it may help if you wish to distinguish multiple layers.

  Opacity: Use the opacity slider to change the opacity of this layer, from transparent to fully opaque.

  Line Color: Use this color selector to set the color of the surface line. Clicking the Select Color... button will bring up a dialog box with a grid of color. Click one to set the color.

  Vertex Color: Use this color selector to set the color of the surface line.

  Line Width: Use this slider to set the width of the surface line.