Anatomical Volumes

Scuba can view multiple anatomical volumes and show them composited in the same space, each with different opacity and thresholding options. Volumes can be treated as anatomical, meaning they are drawn in grayscale, as segmentations, drawn with a color table and each voxel treated as an anatomical labelling, or functional, drawn with a heatscale and with special thresholding options. This section deals with options and controls relating to anatomical volumes, which also generally apply to the other volume types.

Loading Volumes

You can load a volume from the command line or from within the program. From the command line, use the -v option:

scuba -v FILENAME

If you have the SUBJECTS_DIR variable defined, you can use the -s option to declare a subject, and scuba will search for any file names passed to -v in the subject's mri/ directory. These are equivalent:

setenv SUBJECTS_DIR /home/myname/subjects
scuba -s bert -v T1.mgz

scuba -v /home/myname/subjects/bert/mri/T1.mgz

cd /home/myname/subjects/bert/mri
scuba -v T1.mgz

You can also pass in additional options to configure the layer that the volume will be displayed it, e.g.:

scuba -v T1.mgz:brightness=0.5:contrast=20

For example, this line sets the brightness to 0.5 and the contrast to 20. For additonal options you can pass in on the command line, see the ["scuba"] page for command line reference.

Alternatively, you can use the File->Load Volume... menu command from within the program to use a standard dialog box to load a volume. Note that this dialog box also has an option labeled, Automatically add new layer to all views. This is enabled by default. If checked, the layer that will display this volume will be added in the next empty slot to all existing views. This is probably what you want to happen, unless you specially want to exclude this volume from certain views.

Display Options

Like other layer types and data collections, display options for anatomical volumes in the Layers panel, and settings for transforms are in the Data panel.

In the Layers panel, you can configure the following things:

• Layer: This pull-down menu will let you select the layer to configure.

  Name: This editable field lets you change the name of the layer. Initially, the names of the layers are the same as the data collections they are drawing. You don't have to set or change the name, but it may help if you wish to distinguish multiple layers.

  Opacity: Use the opacity slider to change the opacity of this layer, from transparent to fully opaque.

  Color Map: These buttons configure how the layer translates volume values into colors.

  • Grayscale: This will display volumes in grayscale from dark for low values to bright for high values. This is appropriate for anatomical scans.

    Heat scale: The volume values will be drawn. You can use the Heat Scale Min, Mid, and Max fields can be used to configure the heat scale. This is appropriate for functional activation volumes.

    LUT: The volume will be drawn using a look up table. For each value in the volume, an entry in the look up table will specify the color to be used, as well as an anatomical label to be displayed in the label area. This is appropriate for anatomical segmentation volumes.

  LUT: This chooses the LUT to be used if the LUT value is chosen for the Color Map option. You can load additional LUTs from the File menu, and set their names in the Color LUTs panel.

  Draw 0 values clear: Normally, the value of 0 is drawn in whatever is appropriate for the current color map. This checkbox will make all 0 values transparent. It's useful for overlay volumes.

  Draw maximum intensity projection: Instead of drawing a single slice, this option will draw the voxel with the maximum intensity in through plan projection. This takes a while to calculate, so choosing this option will probably show a progress bar, and changing orientations will cause a new projection to be calculated.

  Interpolation method: These buttons set the kind of interpolation used when drawing the volume. The following options are available:

  • Nearest: This rounds volume coordinates to the nearest integer and samples the volume at that point. This is the quickest method, but it looks blocky.

    Trilinear: This option uses trilinear sampling.

    Sinc: This option is the slowest, but the nicest looking interpolation.