Segmentation Volumes

Compared to Anatomical Volumes

For the most part, segmentation volumes are simply anatomical volumes drawn with a LUT instead of in grayscale, and edited with values from a LUT table rather than explicit numerical values. So, it is a good idea to read the [:ScubaGuide/ScubaWorkingWithData/ScubaAnatomicalVolumes ScubaAnatomicalVolume] section first.


Loading segmentation volumes from the menu bar is exactly the same as loading anatomical volumes; you don't even declare it as a segmentation volume until after it is loaded.

You can specify a volume as a segmentation volume from the command line with the colormap option.

scuba -v segmentation.mgh:colormap=lut:drawzeroclear=1:lut=MyLUT

Use the colormap option to specify the lut value. Use the drawzeroclear option set to 1 to tell scuba to draw 0 values transparently, as is appropriate with segmentation volumes. Finally, use the lut option to specify an LUT to use. This will be the label of the LUT loaded. If your LUT is one of the ones loaded automatically by scuba, load up scuba first to see what label is applied to the LUT you wish to load.

If you need to load a new color table, go to the Color LUTs panel, click the Make New LUT button, then click the Browse button to set the file name for your new LUT. Then you may change the label if you'd like.

Display Options

To treat an anatomical volume as a segmentation volume, go to the Layer panel and select the LUT button. This will automatically set the Draw 0 values clear option to on. Then select the LUT to use from the LUT pull-down menu.

Most likely, you will want to enable info display in the label area for segmentation labels, so make sure to stop by the Views panel and check the Inf checkbox in the row that your segmentation volume is in.


Editing segmentation volumes is done with the Voxel Editing and Voxel Filling tools. These are covered in the [:ScubaGuide/ScubaWorkingWithData/ScubaAnatomicalVolumes: ScubaAnatomicalVolume] section.

Histogram Fill

There is a special tool for filling areas of a segmentation volume based on an anatomical volume. This tool displays a histogram of the current slice of an anatomical value and allows you to select ranges of values in that volume, and set the corresponding voxels in the segmentation to a specific label.

To use this tool, have an anatomical volume and a segmentation volume loaded and declared as such, and use the Tools->Histogram Fill... command. In the following dialog box, specify your anatomical and segmentation volume. If you only want to take the histogram of an ROI, choose the ROI.

The histogram will be computed for the current slice. Use the left mouse button to click and drag a range of values. This will create a new region in the histogram as a horizontal bar with a numerical label on it. Below the histogram, a new row will be added for this range, showing the value range and a pull-down menu. Use the pull-down menu to select a segmentation label from the current LUT.

You can click and drag on a region bar with the middle mouse button to move the range, or click with the right button to delete that range.

When you are done declaring ranges, click the OK button, and the values in the current slice of the segmentation will be set.


Saving segmentation volumes is exactly like saving normal anatomical volumes. Just make sure the segmentation volume data collection is the one selected in the Data panel, and use one of the File->Save <data collection>... commands.