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buttons on the right side. Clicking these show the various control buttons on the right side. Clicking these shows the various control

Up to ScubaGuide

Back to [:ScubaGuide/ScubaGeneralUsage: ScubaGeneralUsage]

Continue to [:ScubaGuide/ScubaGeneralUsage/ScubaInterface: ScubaInterface]

Starting Up

Start scuba by typing scuba on the command line. Make sure to have the environment variable FREESURFER_HOME set to a freesurfer installation that includes scuba (FreeSurferDev).

Loading data

You can load data in one of three ways:

Command Line

Specify data to load on the command line with the -s, -v, and -f options. -s will specify a subject. This sets the 'main' subject name for scuba, and all subsequent requests to load data will first look in this subject's data directories. Use -v to load a volume. You can specify an entire path, or a data name in a subject directory, if you have specified -s. Use -f to similarly load surfaces.

You can get a reference by typing scuba --help:

$ scuba --help

Usage: scuba [OPTION]... Data viewer for the FreeSurfer package.

Options: -s, --subject SUBJECT Set the subject for this session. Environment variable

  • SUBJECTS_DIR should be set.

-v, --volume FILE Load a volume file. Can be a file name or a subdir in

  • the subject's directory specified with -s.

-f, --surface FILE Load a surface file Can be a file name or a subdir in

  • the subject's directory specified with -s.


  • scuba -s bert -v T1

Specify bert as the main subject and load bert's T1 volume. This mimics the tkmedit style of 'tkmedit subject volume'.

  • scuba -v $SUBJECTS_DIR/bert/mri/T1

This does the same thing but specifies the volume explicitly.

  • scuba -s bert -v T1 -f lh.white

This also loads a surface.

  • scuba -v $SUBJECTS_DIR/bert/mri/T1 -f $SUBJECTS_DIR/bert/surf/lh.white

This does the same but specifies the files explicitly.

There are also other command line options - check the ["scuba"] usage page for details.

You can also load data through the File menu once scuba is loaded. Scuba, unlike tkmedit, does not need to load data to start up. The file menu contains menu items for loading volumes, surfaces, and labels (which get imported into ROIs).

Subjects Panel

You can load volumes and surfaces from subjects in your SUBJECTS_DIR with the Subjects panel. When you run scuba, you will see a set of buttons on the right side. Clicking these shows the various control panels. The Subjects panel is shown automatically. It scans your SUBJECTS_DIR and puts all subjects and their volumes and surface in pull-down menus. Select the subject name in the first menu, then select a volume or surface and click the Load button next to it.

Viewing Data

Click on the Layers panel to see the settings available for the data you have loaded. You can select the layer you wish to edit with the pull-down menu near the top of the panel area.

Click on the Views panel to see which layers are loaded. Each view has ten slots in which layers are drawn. You can select a different layer to go into a draw level by clicking on the pull-down menu for that level. Layers in higher draw levels will be drawn on top of layers in lower draw levels. Use the checkboxes in the column title Vis to turn a layer's visibility on and off. Check the boxes in the Inf column to turn on information reporting for that level.

If the Inf checkbox for a level is turned on, you will see information about the voxel under the cursor and the mouse in the table underneath the main viewing area. This can be arranged in list mode or table mode using the attachment:icon_label_list.gif and attachment:icon_label_table.gif buttons in the toolbar.

You can switch to a multi-orientation view by clicking the attachment:icon_view_multiple.gif or attachment:icon_view_31.gif buttons in the toolbar. Clicking in any view with the left mouse button will recenter all views around the point you click.

To save a picture of your view, use the File->Save TIFF Capture... command.

ScubaGuide/ScubaGeneralUsage/ScubaQuickStart (last edited 2008-04-29 11:45:31 by localhost)