= 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