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