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.
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 ScubaAnatomicalVolume section.
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.
Segmentation Volume Report
There is a tool for generating report about segmentation structure sizes and included voxels. This is in the Tools->Generate Segmentation Volume Report... command. Before using this tool, you need at least one segmentation volume loaded.
This will bring up a window in which you configure the parameters of the report. At the top, choose a segmentation volume from the pull-down menu. If you would like to include average intensity values for the structures you select, check the checkboxes next to the anatomical volumes for which you would like the information.
Next, select the structures on which you would like to receive information. By default, the same LUT that your segmentation volume uses will be pre-selected in the pull-down menu, but you can change that if you'd like. Double click on the structures in the left list or select them and click the Add structure button to add them to the list of reported structures on the right. To remove structures, double click on them in the right list or select them and click the Remove structure button.
If you would only like the report over in an ROI, click the Only report for ROI checkbox. Then choose a data collection and ROI to which to limit the report.
To generate an additional report that lists all the voxels that are in the structures you have chosen, check the Additional intensity report for individual voxels checkbox.
Then just enter file names for the two reports, and click the OK button.
The main report will be in the following tab delimited format. On the first line, the keyword SUBJ and then a column header for each pair of structures and anatomical volumes you have selected. You will see one column for each structure followed by the structure's average intensity in the anatomical volume. The second line contains the subject name, and then for each column, if it is a structure column, the number of voxels in the structure, or if it is a structure-intensity column, the average intensity in that anatomical volume for the voxels in the structure.
The secondary report will have a column for each structure-anatomical volume pair. In each column, the anatomical voxels in each structure will be listed.
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.