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== Voxel Editing == Volume editing is done with the Voxel Editing tool, which is the attachment:icon_edit_volume.gif, and the Voxel Filling tool, which is the attachment:icon_fill_volume.gif. The options for these tools are in the Tools panel. '''Target Layer''': This sets the layer that changes will be made to. It's very important to check the target layer when making edits, as it can be difficult to tell which layer you are editing if your layers are similar. '''Brush Options''': This sets the shape of your brush. ''Voxel'' will paint just a single voxel, while ''Circle'' and ''Square'' will use the ''Radius'' setting to draw with shaped brush. '''Radius''': This slider sets the size of the ''Circle'' and ''Square'' brushes. The radius is in millimeters, in world space. '''Only brush zero values''': This limits the voxels that can be edited to only those with 0 values. This is useful for editing segmentation values, as it prevents already edited voxels from being re-edited. '''New Value''': This is the value that will be painted when using the middle mouse button. You can set it numerically, or, if the volume is a segmentation volume, use the label values in the list below. '''LUT''': This is the source of the available label values that you can use for the new value if the volume being edited is a segmentation volume. Beneath this is a list of values in the LUT selected. Click on an entry in the list to set the '''New Value''' from the LUT entry. ''Sort'': The LUT entry table can be sorted with the ''Table'' option, to use the order from the LUT file, or with the ''User'' option, that only shows the entries clicked by the user. The ''User'' list can be used to build a list of custom entries, which is useful if your LUT is long and you only want to see a limited selection of entries. Just switch to ''Table'' mode, click on the entries you wish to use, and then switch to ''User'' mode to see only those entries. ''Clear User List'': Use this button to clear the list of entries displayed when the list is in ''User'' mode. '''Erase Value''': This will set the value drawn when the right mouse button is used. By default, it sets voxels to 0. In the case of a segmentation volume, this erases the segmentation label. |
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.
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.
In the Layers panel, you can configure the following things:
Layer: This pull-down menu will let you select the layer to configure.
Name: This editable field lets you change the name of the layer. Initially, the names of the layers are the same as the data collections they are drawing. You don't have to set or change the name, but it may help if you wish to distinguish multiple layers.
Opacity: Use the opacity slider to change the opacity of this layer, from transparent to fully opaque.
Color Map: These buttons configure how the layer translates volume values into colors.
Grayscale: This will display volumes in grayscale from dark for low values to bright for high values. This is appropriate for anatomical scans.
Heat scale: The volume values will be drawn. You can use the Heat Scale Min, Mid, and Max fields can be used to configure the heat scale. This is appropriate for functional activation volumes.
LUT: The volume will be drawn using a look up table. For each value in the volume, an entry in the look up table will specify the color to be used, as well as an anatomical label to be displayed in the label area. This is appropriate for anatomical segmentation volumes.
LUT: This chooses the LUT to be used if the LUT value is chosen for the Color Map option. You can load additional LUTs from the File menu, and set their names in the Color LUTs panel.
Draw 0 values clear: Normally, the value of 0 is drawn in whatever is appropriate for the current color map. This checkbox will make all 0 values transparent. It's useful for overlay volumes.
Interpolation method: These buttons set the kind of interpolation used when drawing the volume. The following options are available:
Nearest: This rounds volume coordinates to the nearest integer and samples the volume at that point. This is the quickest method, but it looks blocky.
Trilinear: This option uses trilinear sampling.
Sinc: This option is the slowest, but the nicest looking interpolation.
Brightness, Contrast: Sets the brightness and contrast, applicable only to grayscale volumes. This can also be set by clicking and dragging if you hold down the shift key and drag with mouse button 1.
Min, Max: Sets the minimum and maximum visible values for volume display. Values below the the minimum value and above the maximum value will not be drawn, so those voxels will be transparent.
Heat Scale: The Min, Mid, and Max values configure the heat scale display. The heat scale is a piecewise linear threshold with two segments: the first from Min to Mid and the second from Mid to Max.
Editable ROI: By default, ROIs belonging to this collection are editable with the ROI tools. Uncheck this option to lock the ROIs to keep them from being edited.
ROI Opacity: This is the translucency for the ROIs associated with the data collection the layer is drawing, which can be controlled separately from the layer opacity.
You can also set display transforms and data transforms that may affect the display of the volume, from the View and Data panels, respectively.
Voxel Editing
Volume editing is done with the Voxel Editing tool, which is the attachment:icon_edit_volume.gif, and the Voxel Filling tool, which is the attachment:icon_fill_volume.gif. The options for these tools are in the Tools panel.
Target Layer: This sets the layer that changes will be made to. It's very important to check the target layer when making edits, as it can be difficult to tell which layer you are editing if your layers are similar.
Brush Options: This sets the shape of your brush. Voxel will paint just a single voxel, while Circle and Square will use the Radius setting to draw with shaped brush.
Radius: This slider sets the size of the Circle and Square brushes. The radius is in millimeters, in world space.
Only brush zero values: This limits the voxels that can be edited to only those with 0 values. This is useful for editing segmentation values, as it prevents already edited voxels from being re-edited.
New Value: This is the value that will be painted when using the middle mouse button. You can set it numerically, or, if the volume is a segmentation volume, use the label values in the list below.
LUT: This is the source of the available label values that you can use for the new value if the volume being edited is a segmentation volume. Beneath this is a list of values in the LUT selected. Click on an entry in the list to set the New Value from the LUT entry.
Sort: The LUT entry table can be sorted with the Table option, to use the order from the LUT file, or with the User option, that only shows the entries clicked by the user. The User list can be used to build a list of custom entries, which is useful if your LUT is long and you only want to see a limited selection of entries. Just switch to Table mode, click on the entries you wish to use, and then switch to User mode to see only those entries.
Clear User List: Use this button to clear the list of entries displayed when the list is in User mode.
Erase Value: This will set the value drawn when the right mouse button is used. By default, it sets voxels to 0. In the case of a segmentation volume, this erases the segmentation label.