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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.

To scroll through your loaded volume, use the 'Page Up' and 'Page Down' keys on your keyboard.

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. Some settings may be disabled if they do not apply to the current mode.

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

You can also set display transforms and data transforms that may affect the display of the volume, from the View and Data panels, respectively.

Grayscale Display

There are several factors that control the grayscale display. The Visible Min and Max control the lowest and highest values that are drawn. Values outside of this range are drawn with intensity 0, and will be translucent if the Draw Zero Values Clear options is on. The Window and Level control the range of values that are mapped to intensities within the Visible range. The Level defines the midpoint, and the Window defines the extent; the darkest value is (Level - (Window/2)) and the brightest value is (Level + (Window/2)). Finally, the Brightness and Contrast define a sigmoid curve inside the visible range to further tweak the intensities. Brightness controls the offset of the curve, bringing it closer to the end of the range defined by the Level and Window. The Contrast defines the sharpness of the curve; a low contrast looks like a straight line, a middle Contrast looks like an S curve, and a high contrast looks more like a stepwise function.

This diagram may help:


Additionally, here is the code to build the lookup table. ScubaGrayscaleCode

Voxel Editing

Volume editing is done with the Voxel Editing tool, which is the icon_edit_volume.gif, and the Voxel Filling tool, which is the icon_fill_volume.gif. The options for these tools are in the Tools panel.

Additionally, if you hold down the shift key while the editing tool is active, you will see a line stretch from the last clicked point to the mouse. If you middle or right click with the shift key still held down, scuba will brush that line with the value corresponding to the mouse button you clicked. You can use this to brush straight lines.

Voxel Filling

Selecting the Voxel Filling tool will show a different set of options in the Tools panel. The filling algorithm starts at a seed point and fills adjacent voxels that are similar to the seed voxel. The degree of similarity is what can be configured with the filling options.

It also contains the same New Value and LUT list as the Voxel Editing tool. See the above section for details.

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.

Saving Volumes

After your careful edits, you will want to save your volume. If using multiple data collections, first make sure it is the currently selected data collection. To do this, go into the Data panel and select your volume from the pull-down menu at the top of the panel. Then use the File->Save command.

There are three versions of the Save command in the File menu. They will all contain the name of the data collection currently selected in the data panel. The Save... command will overwrite the data that you orinally loaded. The Save As... command will save this data with a new name and location, and subsequent Save... commands will save in this new location. The Save Copy As... command will save this data in a new location with a new name, but will continue to work on the original data, that is, subsequent Save... commands will overwrite the original location.

We recommend you save your volume as a .mgh file or a compressed .mgh file, .mgz. Scuba will guess the file type to save based on the format of the file name you choose. To save as a set of COR files, choose a directory as the save target.

ScubaGuide/ScubaWorkingWithData/ScubaAnatomicalVolumes (last edited 2008-04-29 11:45:31 by localhost)