Name

scuba - volume and surface visualizer and editor

Synopsis

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.

-l, --label FILE

Load a label file as an ROI into the most recently loaded volume. Can be a full file name or a fil in the subject's label directory.

-f, --surface FILE [FILE...]

Load a surface 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.

-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:

opacity=FLOAT

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

label=STRING

Sets the label for the layer.

For volume layers:

colormap=TYPE

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

samplemethod=TYPE

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

lut=LUT_NAME

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.

drawzeroclear=1|0

Sets the option for drawing zero values clear.

brightness=FLOAT

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

contrast=FLOAT

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

window=FLOAT

Sets the grayscale window for the layer, from 0 to 1.

level=FLOAT

Sets the grayscale level for the layer, from 0 to 1.

visible=MIN,MAX

Sets the visible value range to MIN and MAX. These are both floats.

visiblemin=FLOAT

Sets the minimum visible value.

visiblemax=FLOAT

Sets the maximum visible value.

heatscale=MIN,MID,MAX

Sets the heat scale threshold values. These are floats.

heatscalemin=FLOAT

Sets the heat scale min threshold value.

heatscalemid=FLOAT

Sets the heat scale mid threshold value.

heatscalemax=FLOAT

Sets the heat scale max threshold value.

heatscaleoffset=FLOAT

Sets the heat scale offset.

frame=INT

Sets the current frame.

For surface layers:

linewidth=INTEGER

Sets the line width of the surface display.

vertexcolor=R,G,B

Sets the color of vertices. R,G,B should be integers from 0-255, e.g. 0,128,255 for no red, medium green, and full blue.

linecolor=R,G,B

Sets the color of vertices. R,G,B should be integers from 0-255, e.g. 0,128,255 for no red, medium green, and full blue.

Description

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

ScubaGuide

Links

FreeSurfer, Scuba

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author

KevinTeich

scuba (last edited 2008-04-29 11:45:46 by localhost)