scuba - volume and surface visualizer and editor


scuba [OPTION]...

Optional Flagged Arguments

-h, --help

Display usage information and exit.

-s, --subject SUBJECT

Set the subject for this session. Environment variable SUBJECTS_DIR should be set.

-v, --volume FILE [FILE...]

Load a volume file. Can be a file name or a subdir in the subject's directory specified with -s. Can specify more than one file name; scuba will keep trying to load them until it reaches another option with a dash in front of it.

-f, --surface FILE

Load a surface file. Can be a file name or a subdir in the subject's directory specified with -s.

-t, --transform FILE

Load a transform file. Can be a file name or a file in the subject's mri/transforms directory specified with -s.

Additionally, you can set some layer-specific options from the command line. These are appended to the file name for the data collection that will be put into a layer in option=value pairs and seperated by colons, for example:

-v VOLUME_FILENAME[:option1[=value1]][:option2[=value2]]...

The currently supported options and values are:

For all layers:


Sets the opacity for the layer. FLOAT should be a value from 0 to 1.

For volume layers:


Sets the color map method for the layer. TYPE should be grayscale, heatscale, or lut.


Sets the sampling method for the layer. TYPE should be nearest, trilinear, or sinc.


Sets the color LUT for the layer (and automatically sets the color map method to lut). The LUT_NAME should be the label of an already loaded LUT. By default scuba loads a few LUTs that it finds, and you can use a script to load others. Just use the name that you see in the pull-down menu in scuba whenever it lists LUTs.


Sets the option for drawing zero values clear.


Sets the brightness for the layer where 1 is dark and 0 is bright.


Sets the contrast for the layer where 0 is all gray and 30 is black/white.


scuba is a unified viewer for the FreeSurfer package. It replaces tkmedit and tksurfer. It displays volumes and surfaces in a common coordinate space and allows the user to apply various viewing parameters and transforms.

Example 1

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'.

Example 2

scuba -v $SUBJECTS_DIR/bert/mri/T1

This does the same thing but specifies the volume explicitly.

Example 3

scuba -s bert -v T1 -f lh.white

This also loads a surface.

Example 4

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

This does the same but specifies the files explicitly.

Example 5

scuba -v T1.mgz:brightness=0.5:contrast=25.0:samplemethod=trilinear

This sets the brightness and contrast for the layer into which T1.mgz will be loaded.

Example 6

scuba -v T1.mgz:brightness=0.5:contrast=25.0:samplemethod=trilinear seg.mgz:lut=tkmeditParcColorsCMA:drawzeroclear=1

This also loads in and configures an additional volume as a segmentation.

See Also



FreeSurfer, ["Scuba"]

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