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
You can load a label file from the command line or from within the program. From the command line, use the -l option after the -v option that loads the volume into which you want to load the label:
scuba -v VOLUME_FILE -l LABEL_FILE
This will load the label file into the most recently loaded volume.
To load a label file from within the program, 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.
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 , and ROI Filling . 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 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.
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.
You can use the Volume ROI Intensity Chart tool to make a chart plotting the intensities in a volume of all voxels in an ROI. To use this tool, you'll need a volume loaded and an ROI drawn. To create the chart, choose the Tools->Make New Volume ROI Intensity Chart... menu command.
In the resulting dialog box, choose a volume, and then choose an ROI from that volume. Click the OK button to make the chart window. A window will open with the values in the ROI you chose plotted with the intensity on the y axis. As you change the ROI, the chart will update to reflect the changes.
You can generate a report of the currently plotted ponints by clicking the Generate Report button in the corner of the chart window. This will show a dialog box allowing you to select the information you want in the report. The report will consist of one row for each voxel plotted, with the columns you choose seperated by a tab character. Enter a file name and click OK to generate the report.
As updating the chart when changing the ROI is computationally intensive, you may want to close the chart window when you are done. You may do this by click the normal close window button.