Volume ROIs

Volume ROIs are associated with the data collection volume for which they were created or into which they were loaded. The ROI is in the resolution of that volume, which is important when saving to a label file.

Multiple ROIs can exist on a data collection. They can be loaded in from a label file, or created and edited manually. They can be saved out as label files.

Creating and Loading

To load an ROI from a label file, use the File->Load Label... command. You will need to choose a data collection into which to load the label. This is very important.

To create a new ROI, use the Make New ROI button in the Data panel. This will create a new ROI associated with the data collection currently displayed in the data panel. Note that when data collections are first loaded, there is an ROI already created.

Display Options

To change the display options of ROIs, use the data panel. The bottom section of the data panel is devoted to ROIs. The menu labeled Current ROI is used to select an ROI. Directly beneath this menu is the ROI ID and the ROI label. You can change the label by typing into the text field.

Under that is a selection of ROI types, Free or Structure. A Free label can be drawn in any color you'd like. A Structure label is assigned an anatomical label from an LUT and is drawn in the color associated with that LUT entry. You can choose the LUT from the pull-down menu below those two buttons, and the LUT entry from the list table below that. At the bottom is the Free Color selector; if the label is designed a Free label, use this color selector to choose a color for the label.

Additionally, there is an ROI Opacity slider for each layer in the Layers panel. This affects the opacity at which the ROI is rendered in that label.


Volume ROIs have analogous editing tools to the volume; ROI Editing attachment:icon_edit_label.gif, and ROI Filling attachment:icon_fill_label.gif. Selecting these tools will show similar options in the Tools panel as the Voxel Editing and Voxel Filling tools, except that the options for setting the new and erase values are not available. Here, clicking with the middle button will draw the ROI, and clicking with the right button will erase it. Please see the [:ScubaGuide/ScubaWorkingWithData/ScubaAnatomicalVolumes: ScubaAnatomicalVolumes] section for details.

By default, all ROIs will be created editable. To disable this, use the Editable ROI checkbox in the Layer panel. Note that this only applies to the currently selected layer; all draw and editing commands go to the selected layer, i.e. the target layer, and ROI editing commands will affect the current ROI in the data collection that the layer is rendering unless this checkbox is disabled.

Undoing Edits

Note that all edits and fills are undoable with the File->Undo command. All undone actions are then redoable in a stacking fashion.


To save an ROI as a label file, go to the data panel, select the data collection to which the ROI belongs, the select the ROI from the Current ROI menu, and then use the File->Save Label... menu command.

You can also export all the segmentation ROIs in a collection as a segmentation volume with the File->Export ROIs as Segmentation... command. If this is confusing, here is the process: A segmentation volume is created the same size as the anatomical volume, and for every structure ROI in the data collection, every voxel in that ROI is set to the same structure value in the segmentation volume. Note that only ROIs marked as segmentations are exported, and for ROIs that overlap, the ROI with the highest ID will "win" the placement in the segmentation volume.