Caret6:Documentation/UserInterface/DisplayControlWindow

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Contents

Display Control Dialog

Overlay/Underlay - Surface Page

This page controls the surface data overlays. The controls for a single overlay are in a single row.

  • Overlay - Name of the overlay.
  • Data Type - Selects the type of data for an overlay.
  • Opacity - Controls the opacity of the overlay and this value ranges from zero (fully transparent) to one (fully opaque).
  • Display Column - Selects the column of data for the selected overlay Data Type.

Multiple Structure Coloring

If there is more than one structure loaded, the names of all columns for a data type are placed in the controls. When an overlay is set, say Labels named "Brodmann", Caret will examine the label file in each structure (left, right, etc) for a column named Brodmann. If the column is found, the surface is painted with Brodmann. If the column is not found, the surface receives no painting for the overlay.

To see which data columns are loaded for each of the structures visit the Label Selection, Metric Selection, or Shape Selection pages. Each of these pages lists all of the columns that are loaded and a list of structures that contain the data column.

Overlay/Underlay - Volume Page

This page controls the data displayed on volume slices.

  • Overlay - Name of the overlay.
  • Data Type - Selects the type of data for an overlay.
  • Opacity - Controls the opacity of the overlay and this value ranges from zero (fully transparent) to one (fully opaque).
  • Display Volume - Selects the volume for the selected overlay Data Type.

All Structures View Page

Surfaces

Controls the surfaces that are displayed in the All Structures View. One surface from each structure may be selected for display.

Volume

Controls the display of volume data in the All Structures View.

  • Slices - displays slices for overlays that are not set to None on the Overlay/Underlay - Surface page.
  • Cloud - Displays the voxels as 3D boxes for the overlays not set to None.

Annotation Main Page

  • Show Annotations - Enables the display of annotations.
  • Show Text Background - If selected, a background is drawn behind the text. If not selected, anything behind the text shows through the text.

Annotation Class Page

  • All On - Pressing this button enables the display of all Annotation classes.
  • All Off - Pressing this button disables the display of all Annotation classes.

Show Annotations Without Class Assignments - If checked Annotations without a class assignment are displayed.

Border Main Page

Controls the display of borders.

  • Show Borders - Controls the display of borders.
  • Show as Symbols - Controls the display of a sphere at each border point.
  • Show as Lines - Controls the display of lines that connect adjacent points in borders.
  • Show Raised Borders (flat) - Borders on flat surfaces are forced to be just above flat surfaces.
  • Show First Link Red - Shows the first point in the border in red.
  • Line Width - Controls the width of lines that draw borders.
  • Opacity - Controls the opacity of the border symbols and lines.
  • Point Size - Controls the size of the symbols displayed for border points.
  • Unstretched Lines Factor - On flat surfaces some borders drawn as lines may have lines that connect distance regions that are separated by cuts. This control affects how much "stretching" is allowed that prevents these borders from being drawn.

Border Color Page

Only borders whose colors are selected on this page are displayed.

  • All On - Pressing this button selects all colors.
  • All Off - Pressing this button deselects all colors.
  • Colorize Labels - If selected, the border color labels are drawn using the corresponding border color.

Border Name Page

Only borders whose names are selected on this page are displayed.

  • All On - Pressing this button selects all names.
  • All Off - Pressing this button deselects all names.
  • Colorize Labels - If selected, the border name labels are drawn using the assigned border color.

Brain Tips

In Caret's graphical user-interface, one can move the mouse over a control, and if the mouse remains still for a short period of time, a Tool Tip describing the control is displayed. Brain Tips can display information about the location in the brain under the mouse.

Surface Node Brain Tips

These controls allow the selection of overlay data display in Brain Tips. If more than one surface node brain tip is enabled, they are separated by a colon (:) in the brain tip.

Layer Brain Tips

  • Borders - Enable border brain tips which displays the name of the border under the mouse.
  • Foci - Enable foci brain tips which displays the name of the focus under the mouse.


Connectivity Color Mapping Page

These controls allow one to set the color mapping for each of the Connectivity Selectors.

Color Mapping

The color mapping controls are used to control how connectivity values are mapped to colors in the color palette. The color palette consists of a set of colors and each color has an associated scalar value ranging from negative one to positive one. The color mapping controls determine how connectivity values are mapped into the color palette for the coloring of connectivity data. Depending upon the settings, a positive connectivity value is mapped to zero in the color palette, another positive connectivity value is mapped to positive one in the color palette, a negative connectivity value is mapped to zero in the color palette, and another negative connectivity value is mapped to negative one in the color palette.

  • Auto Scale - The most negative connectivity value is mapped to negative one in the color palette, the zero connectivity value is mapped to zero in the color palette, and the most positive connectivity value is mapped to positive one in the color palette.
  • Auto Scale Percentage - All of the connectivity values are sorted the negative and positive values are handled separately. The values entered for Pos Min and Pos Max are percentages of the total number nodes with positive connectivity values. So, if the Pos Min value is 2, the algorithm finds a positive connectivity value "MINP" such that 2% of all positive connectivity values are less than "MINP" and the value "MINP" is mapped to zero in the color palette. Similarly, if Pos Max is 98, the algorithm find a positive connectivity value "MAXP" such that 98% of all positive connectivity values are less than "MAXP" and the value "MAXP" is mapped to positive one in the color palette. The mode of color mapping may be useful if there are positive or negative "outliers" that skew the color mapping.
  • User Scale - Neg Max is mapped to negative one in the color palette, Neg Min is mapped to zero in the color palette, Pos Min is mapped to zero in the color palette, and Pos Max is mapped to positive one in the color palette.

Debugging Page

Foci Main Page

  • Show Foci - Controls the display of all foci.
  • Show Volume Foci - Controls the display of foci on volume slices.
  • Show Foci Pasted Onto 3D Surfaces - If selected, any foci "floating" above a surface are pulled onto the surface.
  • If selected, foci that ambiguous to multiple structures are only displayed on the "best" structure.
  • Foci Size - Controls the size of the foci symbols.
  • Opacity - Controls the opacity of foci symbols (zero is fully transparent, one is fully opaque).
  • Distance - ???
  • Coloring Mode - Chooses colors using either the foci names or classes.

Foci Class Page

Only foci whose classes are selected on this page are displayed.

  • All On - Pressing this button selects all class names.
  • All Off - Pressing this button deselects all class names.
  • Show Foci Without Class Assignments - If selected, foci that do not have an associated class are displayed.

Foci Color Page

Only foci whose colors are selected on this page are displayed.

  • All On - Pressing this button selects all colors.
  • All Off - Pressing this button deselects all colors.
  • Colorize Labels - If selected, the border name labels are drawn using the foci color.
  • Show Foci Without Color Assignments - If selected, foci missing colors are displayed.

Foci Keywords Page

Only foci whose keywords are selected on this page are displayed. Keywords come from the linked study in the Study Metadata File.

  • All On - Pressing this button selects all keywords.
  • All Off - Pressing this button deselects all keywords.
  • Show Foci Without Links to Studies With Keywords - If selected, foci not linked to studies with keywords are displayed.

Foci Name Page

Only foci whose names are selected on this page are displayed.

  • All On - Pressing this button selects all names.
  • All Off - Pressing this button deselects all names.
  • Colorize Labels - If selected, the foci name labels are drawn using the assigned foci color.

Foci Search Page

This page is used to search foci.

Foci Tables Page

Only foci whose tables are selected on this page are displayed. Tables come from the linked study in the Study Metadata File.

  • All On - Pressing this button selects all tables.
  • All Off - Pressing this button deselects all tables.
  • Show Foci Without Links to Table Subheaders - If selected, foci not linked to table subheaders are displayed.

Label Main Page

  • Geography Blending - Controls the darkening of sulci when an overlay is set to geography blending.
  • Medial Wall Override - If selected and the chosen label column contains the label MEDIAL.WALL, any nodes that have this label are always drawn using the MEDIAL.WALL label color.

Label Name Page

Only labels whose names are selected on this page are displayed.

  • All On - Pressing this button selects all label names.
  • All Off - Pressing this button deselects all label names.
  • Colorize Labels - If selected, the label names are drawn using the assigned label color.

Label Selection Page

This page allows the user to select the label column for each overlay.

  • # - The index of the label column.
  • P - Primary Overlay
  • S - Secondary Overlay
  • T - Tertiary Overlay.
  • (Additional Overlays)...
  • U - Underlay.
  • Structure - A comma separated list of the structure that contain a data column with the column name.
  • Column Name - Name of the column.

Metric Display - Selection Page

This page allows the user to select the metric column for each overlay.

  • # - The index of the metric column.
  • P - Primary Overlay
  • S - Secondary Overlay
  • T - Tertiary Overlay.
  • (Additional Overlays)...
  • U - Underlay.
  • Structure - A comma separated list of the structure that contain a data column with the column name.
  • Column Name - Name of the column.

Metric Color Mapping

Metric Data Column Selection

Each metric data column contains its own parameters for color mapping. Use the controls in this this section to choose the structure and the metric column for that structure.

  • Structure - Chooses the structure for which color mapping is edited.
  • Metric Column - Choose the metric column in the selected structure for editing of color mapping data.

Color Mapping

The color mapping controls are used to control how metric values are mapped to colors in the color palette. The color palette consists of a set of colors and each color has an associated scalar value ranging from negative one to positive one. The color mapping controls determine how metric values are mapped into the color palette for the coloring of metric data. Depending upon the settings, a positive metric value is mapped to zero in the color palette, another positive metric value is mapped to positive one in the color palette, a negative metric value is mapped to zero in the color palette, and another negative metric value is mapped to negative one in the color palette.

  • Auto Scale - The most negative metric value is mapped to negative one in the color palette, the zero metric value is mapped to zero in the color palette, and the most positive metric value is mapped to positive one in the color palette.
  • Auto Scale Percentage - All of the metric values are sorted the negative and positive values are handled separately. The values entered for Pos Min and Pos Max are percentages of the total number nodes with positive metric values. So, if the Pos Min value is 2, the algorithm finds a positive metric value "MINP" such that 2% of all positive metric values are less than "MINP" and the value "MINP" is mapped to zero in the color palette. Similarly, if Pos Max is 98, the algorithm find a positive metric value "MAXP" such that 98% of all positive metric values are less than "MAXP" and the value "MAXP" is mapped to positive one in the color palette. The mode of color mapping may be useful if there are positive or negative "outliers" that skew the color mapping.
  • User Scale - Neg Max is mapped to negative one in the color palette, Neg Min is mapped to zero in the color palette, Pos Min is mapped to zero in the color palette, and Pos Max is mapped to positive one in the color palette.

Note that if Auto Scale or Auto Scale Percentage is selected and more than one overlay displays metric data, the coloring applied to the same value in different overlays may be colored differently. When displaying multiple overlays as metric, it is best to use User Scale with the same settings for all columns.

Display Mode

  • Positive - If checked, positive metric values are displayed.
  • Zero - If checked, zero metric values are displayed.
  • Negative - If checked, negative metric values are displayed.

Palette Options

  • Palette - Chooses the color palette that is used for displaying metric data.
  • Interpolate - If checked, colors are interpolated when a metric value falls between two palette colors in the color palette.

Threshold Selection

Metric Column (Functional Volume) Button - Press this button to select the metric column (functional volume) that is used for thresholding.

  • Off - No thresholding.
  • Normal - Use thresholds entered in this row of the panel.
  • Mapped - Use thresholds provided when the functional volume was mapped to the surface producing this metric column.
  • Mapped Average Area - Use the mapped threshold when the functional volume was mapped to the PALS atlas creating this metric column. This threshold is the Mapped threshold after adjustment so that the surface area covered by averaged mapping approximates the average of the surface from mapping to the individuals in the PALS atlas.
  • Show Mapped Average Area Threshold Failures in Green - This option only applies if Mapped is selected for thresholding. Nodes with values between the Mapped and Mapped Average Area thresholds are shown in green.

Comparison

  • Greater Than - The threshold test is past and data is displayed when the threshold datum is more negative than the negative threshold or more positive than the positive threshold. This mode is useful when the threshold data contains Q-Values (ie: Q >= 0.95).
  • Less Than - The threshold test is past and data is displayed when the threshold datum is less negative than the negative threshold AND less positive than the positive threshold. This mode is useful when the threshold data contains P-Values (ie: P <= 0.05).

Display Color Bar On

If an Overlay box is checked and the corresponding Surface Overlay is set to Metric, a color bar is displayed in the Main Window.

Scenes Page

Scenes - Generic Page

Scene Selection - This box lists the available scenes. To display a scene, either double click the scene name or select the scene name and then press the Apply button.

Selected Scene Description - Contains a description of the selected scene.

Buttons

  • New Scene - Launches a scene editor for creating a new scene.
  • Edit Scene - Launches a scene editor for editing the selected scene.
  • Delete - Deletes the selected scene.

Surface Clipping Page

Surface clipping allows the user to display a geometric subset of a surface or surfaces. Clipping can reproduce the "section" capability that was in Caret5 but is not in Caret6.

Apply Clipping

  • All Surfaces - All surfaces are clipped.
  • Anatomical Surfaces - Clipping is applied to all displayed anatomical surfaces.
  • Main Window - clipping is limited to the surface in the Main Window.

Clipping

  • Negative X - If checked, nodes with X-coordinates less than this value are not displayed.
  • Positive X - If checked, nodes with X-coordinates greater than this value are not displayed.
  • Negative Y - If checked, nodes with Y-coordinates less than this value are not displayed.
  • Positive Y - If checked, nodes with Y-coordinates greater than this value are not displayed.
  • Negative Z - If checked, nodes with Z-coordinates less than this value are not displayed.
  • Positive Z - If checked, nodes with Z-coordinates greater than this value are not displayed.

Surface Drawing Page

Surface Drawing Attributes

  • Drawing Mode - Controls how the surfaces are drawn.
  • Brightness - Adjust the brightness of the surface.
  • Contrast - Adjust the contrast of the surface.
  • Opacity - Adjust the transparency of the surface. A semi-transparent surface may be useful for visualization of foci that are within (under) the surface.
  • Node Size - Adjusts the size of the symbols when the surfaces is drawn as nodes.
  • Link Size - Adjusts the size of links when the surface is drawn using links (connections between nodes).
  • Identify Node Color - Sets the color of the symbol placed on identified nodes.

Surface Node Attributes

  • Show Crossovers - Shows surface crossovers that were determined using Surface Menu->Crossover Check.
  • Show Surface Normals - Shows the surface normals as small vectors.
  • Show Morphing Angular Forces - Shows the morphing angular forces as vectors in green.
  • Show Morphing Linear Forces - Shows the morphing linear forces as vectors in red.
  • Show Morphing Total Forces - Shows the morphing total forces as vectors in blue.
  • Force Vector Length - Scales morphing vectors by this amount.

Surface Axes

  • Show Axes - Shows axes lines.
  • Show Axes Orientation Labels - Shows labels indicating orientation at the end of the axis lines.
  • Show Axes Tick Marks - Shows tick marks along the axes lines.
  • Axes Length - The length of the axes lines.
  • Axes Offset - Offset of the axes from the origin.

Surface and Volume Interaction Page

This page is used to select the surfaces that are used for surface and volume interaction. For instance, if the user selects a voxel, a node identification symbol is displayed on the surface nearest this voxel (with some tolerance). In addition, if the user selects a node on any surface for a structure, the surface selected on this page for the structure is used to determine the corresponding voxel in the volume.

Surface Shape Color Mapping Page

Shape Data Column Selection

Each shape data column contains its own parameters for color mapping. Use the controls in this this section to choose the structure and the metric column for that structure.

  • Structure - Chooses the structure for which color mapping is edited.
  • Shape Column - Choose the shape column in the selected structure for editing of color mapping data.

Other Controls

The color mapping options function just like the Metric Color Mapping controls.

Surface Shape Selection Page

This page allows the user to select the surface shape column for each overlay.

  • # - The index of the surface shape column.
  • P - Primary Overlay
  • S - Secondary Overlay
  • T - Tertiary Overlay.
  • (Additional Overlays)...
  • U - Underlay.
  • Structure - A comma separated list of the structure that contain a data column with the column name.
  • Column Name - Name of the column.

Surface Shape Settings Page

Min/Max Mapping

  • Column - Chooses the column whose data and mapping values are displayed below.
  • Maximum - Shows how the maximum shape values is mapped to the color mapping.
  • Minimum - Shows how the minimum shape values is mapped to the color mapping.
  • Histogram - Shows a histogram of the selected column's data.

Color Mapping

  • Gray - Colors shape data with a gray-scale pattern.
  • Orange-Yellow - Colors shape data with an orange/yellow pattern.
  • Palette - Uses a palette from the Palette File to color shape data.
  • Interpolate Palette Colors - If a color palette is used to color shape data, the colors are interpolated when a shape value falls between two colors in the color palette.
  • Display Palette Color Bar - Displays a color bar in the bottom left corner of the main window showing how shape data is mapped into the color palette.


Enable Node ID Deviation - If a shape column contains a deviation measurement, that deviation can be represented in the size of the identification symbols placed on nodes when they are identified.

Vector Selection Page

Chooses the vector files that are displayed.

Vector Settings Page

Surface Display

  • Display Mode - Displays all vectors (ALL), a subset of vectors (Sparse), or no vectors (None) on surfaces.
  • Symbol - Controls the symbol displayed for a vector.
  • Line Width - Width of line symbols.

Volume Display

  • Display Mode - Displays all vectors (ALL), a subset of vectors (Sparse), or no vectors (None) on surfaces.
  • Slice Above Limit - When displaying vectors on slices, this value determines the distance a vector may be above the slice and still be displayed.
  • Slice Below Limit - When displaying vectors on slices, this value determines the distance a vector may be below the slice and still be displayed.

Drawing

  • Coloring Mode - Vectors may be colored using the color from the vector file or with a Red, Green, Blue coloring scheme that reflects the vector's X, Y, and Z-components.
  • Vector Type - Bidirectional vectors have no orientation and are displayed as a line with the line centered at the vector's origin. Unidirectional Arrow displays vector using an arrow symbol with the origin of the arrow a the vector's origin. Unidirectional Cylinder is link Unidirectional Arrow except that no arrowhead is displayed.
  • Sparse Index Skip - Displays the number of indices skipped when Surface Display Mode or Volume Display Mode is Sparse.
  • Length Multiplier - Multiplies vectors by this amount to exaggerate their true length.

Orientation Filtering

  • Axis - If Any, no filtering occurs. If Left/Right, only vectors whose angle from the X-Axis is less than the "Angle" value are displayed. If Posterior/Anterior, only vectors whose angle from the Y-Axis is less than the "Angle" value are displayed. If Inferior/Superior, only vectors whose angle from the Z-Axis is less than the "Angle" value are displayed.
  • Angle - This value controls the allowable difference between a vector and a selected Axis.

Magnitude

  • Draw With Magnitude - The vector lengths reflect the vector's magnitude.
  • Threshold - Vectors whose magnitude is less than this value are not displayed.

Functional Volume Masking

Functional volume masking is used to limit the display of vectors to those that fall within a functional volume voxel whose value is within the specified range of values.

  • Enable Functional Mask - Enables functional volume masking for vector display.
  • Volume - Volume used for masking vectors.
  • Neg/Pos Threshold - Range of functional values that allow vector display.

Segmentation Volume Masking

Segmentation volume masking is used to limit the display of vectors to those that fall within a segmentation volume voxels whose value is non-zero.

  • Enable Segmentation Mask - Enables segmentation volume masking for vector display.
  • Volume - Volume used for masking vectors.

Volume Drawing Page

Anatomy Volume

  • Brightness - Controls the brightness of the drawn volume.
  • Contrast - Controls the contrast of the drawn volume.
  • Coloring
    • 0 to 255 - Maps a zero voxel value to black and a value of 255 to white.
    • Min to Max - Maps the smallest voxel value to black and the largest voxel value to white.
    • 2% to 98% - The voxel values are ranked such that the voxel that is greater than 2% of the voxel values is mapped to black and the voxel value that is greater than 98% of voxel values is mapped to white.

Segmentation Volume

  • Opacity - Sets the opacity of segmentation volume voxels so that the underlaying anatomy is visible.

Crosshairs

  • Show Crosshairs - Controls the display of crosshairs.
  • Show Crosshair Coordinates - The the coordinates of the crosshairs.

Volume Functional Page

Functional Volume Selection

Use the control to select a functional volume for editing its color mapping parameters. Each functional volume maintains its own set of color mapping parameters.

Other Controls

The color mapping options function just like the Metric Color Mapping controls.

Volume Surface Outline Page

This page controls the display of surfaces drawn as outlines over the volume slices.

  • Show - Enables a surface outline.
  • Color - Color used for surface outline.
  • Thickness - Thickness of the surface outline.
  • Structure - Structure from which the surface is obtained.
  • Surface - Surface whose outline is drawn.
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