Display Control Dialog


A Note About Node Based Files


This documentation often refers to "columns" in relation to node-based files such as paint and metric files.  You can think of these node-based files being represented by a spreadsheet or two-dimensional matrix where each row represents the data for a single node and each column represents a set of data for all of the nodes.  For example a paint file column named geography identifies all nodes' sulcal/gyral status.

Page Selection

Pages are selected using the combo box (pop-up menu) to the right of "Page Selection" at the top of the Display Control Dialog.  Directly to the right of Page Selection are left and right arrows.  These arrows function similar to the back and forward buttons in a web browser.

Available Pages

Overlay/Underlay Surface
Overlay/Underlay Volume
Areal Estimation
Border Main
Border Color
Border Name
Cell Main
Cell Class
Cell Color
CoCoMac Display
CoCoMac Information
Contour Main
Contour Class
Contour Color
Deformation Field
Foci Main
Foci Class
Foci Color
Foci Keyword
Foci Name
Foci Search
Foci Table
Geodesic
Images
LatLon
Metric Miscellaneous
Metric Selection
Metric Settings
Models Main
Models Settings
Paint Main
Paint Column
Paint Names
Prob Atlas Surface Main
Prob Atlas Surface Area
Prob Atlas Surface Channel
Prob Atlas Volume Main
Prob Atlas Volume Area
Prob Atlas Volume Channel
Region
RGB Paint
Scene
Section
Shape Selection
Shape Settings
Surface and Volume
Surface Clipping
Surface Misc
Topography
Vector Selection
Vector Settings
Volume Settings
Volume Surface Outline

Surface Coloration Applies To  Group


Surface (Not always displayed)

When assigning colors to the surfaces, this selection determines if the new selections made on the Display Control Dialog apply to all surfaces or to specific surfaces.

Overlay (Not always displayed)

When assigning colors to the surfaces, this controls which overlay to which the changes apply.

Apply (Data Type) L-to-L, R-to-R Matching to Coord Files

If a metric or shape column is selected, and this option is checked, and the column name contains "left" or "right" in its name, and, there is another column which is the same except that it has "right" or "left" in its name, the "left" column will be applied to LEFT hemisphere surfaces and the "right" column will be applied to RIGHT surfaces.


Overlay/Underlay Surface Page


This page is used to select the type of data that colors the surfaces.  When coloring a surface node, the primary overlay overrides the secondary overlay which overrides the tertiary overlay which overrides the underlay.

Primary/Secondary/Tertiary Overlay or Underlay


Each overlays section contains a set of controls.  The controls displayed vary depending upon the selected data type.

Data Type - Selects the data type for the overlay.

Display Column - For data types (Areal Estimation, Metric, Paint, RGB Paint, Surface Shape, and Topography) that contain multiple columns, this control selects the data column for display.

Threshold Column - For data types (Metric) that contain multiple columns, this control selects the thresholding column.

Lighting - Controls the use of lighting on three-dimensional surfaces for this overlay.  Lighting alters the node coloring, so, in some cases such as the display of functional data, it may be desirable to turn lighting off.

Opacity - Controls the opacity (blending) of this overlay and the data beneath it.  1.0 is opaque and 0.0 is transparent.  The overlay and underlay are blended with the formula node color = (opacity * overlay-color + (1.0 - opacity) * underlay-color).


Types of Data

Coloring Mode

Layers

Overlay/Underlay Volume Selection Page


This page is used to select the type of data that colors volume slices.  When coloring a voxel, the primary overlay overrides the secondary overlay which overrides the underlay.

The right-most part of this page contains combo box (popup-menus) which allow the selection of a column in a specified data type.  The "?" button pops up a dialog containing metadata for the corresponding data type.

Anatomy  Anatomical data that shows the structure of the brain.

Functional-View  Functional data for viewing.

Functional-Thesh  Functional data for thesholding.

Paint  Labels identifying voxels.

Prob Atlas   Colors the voxels in a probabilistic fashion where each probabilistic volume file contains the same type of data (such as sulcal identification) but from different subjects.

RGB  Red, green, blue data coloring applied to the voxels.

Segmentation  A volume where non-zero voxels represent a structure, such as the cortex that has been identified in an anatomical volume and is reconstructed into a surface.  Segmentation voxels are shown in red.

Vector  Essentially an RGB volume where red, green, and blue represent the X, Y, and Z magnitudes respectively.


Areal Estimation Page


Allows selection of the area estimation file column, display of metadata for each column (the "?" pushbutton), and editing of the column names.

Display Color Key  Shows a color key for the currently selected Areal Estimation file column.

Border Main Page


Border Main


Show Borders  Controls the display of borders.

Show Raised Borders (flat surface only) Forces all borders slightly above a flat surface and is used since border projection may sometimes place borders under a surface.

Show Uncertainty Vectors  An uncertainty value may be associated with each border and selection of this item will show an uncertainty vector at each border point.  These uncertainty values are used during the creation of areal estimation data.

Show First Link Red  Shows the first point in a border in red.  This option is often used when viewing registration borders to verify that corresponding borders are drawn in the same orientation.

Override Border Colors with Area Colors  Allows the application of area colors when drawing borders instead of the usual border colors.

Draw Borders Method Control  Draw Borders As Points draws the borders as small point symbol.  Draw Borders as Lines draws the borders as a series of line segments.  Draw Borders as Points and Lines draw the borders as both points and lines.  Draw Borders as Unstretched Lines draws the borders as a series of line segments but elminates line segments on flat surfaces that are substantially longer that the corresponding line segments on fiducial surfaces.  Draw Borders Showing Variability draws borders as points where the thickness represents a variablity associated with the border.  Draw Borders Showing Variability and Lines draw the borders as lines and points where the thickness represents a variablity associated with the border.  The variability is set when an "average border" is created with the Layers Menu->Borders->Create Average Border Dialog.

Border Line Width / Point Size  Controls the size/width of borders points and lines.

Opacity  Controls transparency of border symbols and lines.  1.0=opaque, 0.0=transparent.

Unstretched Lines Factor  Ratio of fiducial to flat border segment length used then drawing borders as unstretched lines.

Display Color Key  Shows a color key of the border colors.

Border Name Page


This page allows the user to control the display of borders based upon the border names.

Border Color Page


This page allows the user to control the display of borders based upon the colors assigned to the borders.

Cell Main Page

Show Cells  Controls the display of cells.

Show Volume Cells  Controls the display of volume cells.

Show Raised Cells (flat surfaces only)   Since some cells are subcortical they may be under the flat surface.  Selecting this option will display the cells on top of the flat surface.

Show Cells on Correct Hemisphere Only  If selected, this inhibits the display of cells that are in the hemisphere that is not displayed.

Deep/Superficial Control   Show Deep and Superficial Cells allows the display of all cells.  Show Deep Cells Only only allows the display of cells that are subcortical (under the surface).  Show Superficial Cells Only only allows display of cells that are above the surface.

Symbol Override  If a value other than NONE, all cells are displayed using the selected symbol.

Cell Size  The size of the cell symbols are multiplied by this value.

Opacity  Controls transparency of cell symbols.  1.0=opaque, 0.0=transparent.

Distance  Cells whose distance from the surface is greater than this amount are not displayed.

Display Color Key  Shows the color key for cells.

Cell Class Page


Controls the display of cells based upon the selected cell classes.

Cell Color Page


Controls the display of cells based upon the selected cell colors.


CoCoMac Display Page


This page controls the display of CoCoMac data.

View Connection

Afferent - Shows areas that connect to the selected area.
Efferent - Shows areas that receive a connection from the selected area.
Afferent and Efferent - Shows areas that are both afferent and efferent with the selected area.
Afferent or Efferent - Shows areas that are afferent or efferent with the selected area.

Paint Column - Selects the paint column that is used with the CoCoMac data file to show afferent and efferent connections.

CoCoMac Information Page

Displays information about CoCoMac connections.

Contour Page


Draw Mode  Points shows the contours as a series of points.  Lines shows the contours as a series of line segments.  Points and Lines shows the contours as both points and lines.

Point Size  Controls the size of contour points.

Line Size  Controls the width of contour lines.

Show First Point In Each Contour In Red  Shows the first point in each contour in red.

Show Contour Cells  Enables the display of contour cells.

Cell Size Cell symbols are multiplied by this value.

Contour Class Page


Enables selection of contour cells using the cells' classes.

Contour Color Page


Enables selection of contour cells using cells' colors.

Deformation Field Page


Options Group


This page controls the display of deformation field data which are vectors originating at each node.  The vectors originate at a node and end at the barycentric coordinate of three nodes.

Column  Selects the deformation field column for display.

Display Mode  All results in all vectors being displayed simultaneously.  None inhibits the display of deformation field vectors.  Sparse displays every "Sparse Distance" number vector.

Sparse Distance  Used to skip nodes when the Display Mode is Sparse.

Show Vectors On Identified Nodes  Enables the display of vectors on nodes that are subsequently selected.

Show Unstretched on Flag Surface  Inhibits display of vectors that would be unusually long on the flat surface due to cuts and the flattening of the surface.

Foci Main Page

Show Foci  Enables the display of Foci.

Show Volume Foci  Enables the display of volume foci.

Show Raised Foci on Flat Surfaces  Since some foci may be subcortical they will appear under a flat surface.  Enabling this option will show the foci on top of the flat surface.

Show Foci Pasted Onto 3D Surfaces  Enabling this option will "paste" foci onto 3D surfaces.  Use of this option will help expose subcortical foci.

Show Foci on Correct Hemisphere Only  Limit the display of foci to those that are associated with the hemisphere that is being displayed.  If the focus has an invalid hemisphere it will always be displayed.

Symbol Override  If a value other than NONE, all foci are displayed using the assigned symbol.  Symbols are part of the focus' color and can be set  using the foci color editor.

Coloring Mode  Determines if foci are assigned a color using the name of the focus or the class of the focus.

Foci Size  Foci symbol size is multiplied by this value.  The focus' size is from the foci color and can be set using the foci color editor.

Opacity  Controls transparency of foci symbols.  1.0=opaque, 0.0=transparent.

Distance  Foci whose distance from the assigned surface is greater than this amount are not displayed.

Display Color Key  Displays a color key for the Foci.  The color key displays each focus color name and a small swatch of the color.

Foci Class Page

Lists all foci classes and allows selection of individual classes for display.

Foci Color Page

Lists all foci colors and allows selection of individual colors for display.

Foci Name Page

Lists all foci names and allows selection of individual foci for display.

Foci Keywords Page

Lists all study keywords and allows selection of individual keywords.  If a focus is linked to a study, at least on of the study's keywords must be selected to enable the display of the focus.

Foci Search Page

The foci search page enables the display of foci that meet search parameters.

Search Set Selection

Search Number - Pressing this button pops up a dialog containing the names of all foci search sets to allow the selection of a foci search set by its name.

Delete Selected Search Set - Pressing this button deletes the selected foci search set.

Add New Search Set - Pressing this button adds a new search set.

Copy Search Set - Pressing this button creates a new search set that is a copy of the currently selected search set.

Search Foci Operations

Search All - Pressing this button applies the selected foci search set to all foci.

Search Displayed - Pressing this button applies the selected foci search set to all displayed foci.

Reset - Pressing this button resets any currently applied foci searches.

Search Parameters

The Search Parameters section contains the parameters of a foci search set.  Each search parameter consists of two rows of controls.  The top row contains the search parameter number, a "+" button for adding a new parameter, a "-" button for removing the parameter, a Logic control a Category control, and a Matching control.  The second row contains a Terms button and a line edit for the search parameters.

The Logic control determines how this search parameter is combined with the previous search parameter.  If Intersection is selected, a focus must meet this search parameter and the previous search parameters.  If Union is selected, the focus must meet the previous search parameter, this search parameter, or both.

The Category control selects the focus or study category (attribute) that is searched.  These categories consist of focus and study attributes.

Matching selects how the terms (in the second row) are applied when searching the category.  ANY of requires at least one of the search terms in in the selected category.  All of requires that all of the search terms are in the selected category.  NONE of requires that none of the search terms are in the selected category.  EXACT PHRASE requires that search term is identical to the selected category.  If the attribute is empty, a NONE_OF search is true, all others are false.

In the second row, pressing the Terms button displays a dialog for assistance with selecting search terms.  The search terms are placed in the line edit with each search term separated by a semi-colon.

Foci Tables Page

List all study tables and allows selection of individual tables.  If a focus is linked to a study, at least one of the study's tables must be selected to enable display of the focus.

Geodesic Page


Enable Geodesic Path for Identified Nodes  If a node is identified, the shorted geodesic distance path to the root node from identified node is displayed.

Show Root Node  Shows a round symbol at the root node (the node used for the geodesic calculation).

Path Line Width  Width of line segments used for the path when Enable Geodesic Path For Identified Nodes is enabled.

The remaining part of the page enabled selection of the available geodesic columns.  Pressing the "?" button will display metadata for the geodesic column.

Images Page


Show Image In Main Window  If checked, the selected image is shown as the background in the Main Window.

The remaining part of the page lists the available images.

Lat/Lon Page


This page allows the user to change the names of latitude longitude file columns.  Pressing the "?" button will show metadata for the corresponding file column.

Metric Miscellaneous

Animation Group

Animate Pushing this button results in the each column of the metric file being applied to the surface.  This may be useful for the display of timecourse data.  A movie can be created by using the Recording Dialog.

Interpolate Frames  If greater than zero, additional surface colorings that are linearly interpolated between two successive metric columns will be displayed.

Popup Graph When Node Identified Group


Show  If not set to Off and a node is identified, a graph will popup showing the metric values for the selected node.

Manual Scaling  Controls the Y-Axis of the popup graph.  If checked, the minimum and maximum values to the right of the Manual Scaling legend are used for the Y-Axis of the graph.  If unchecked, the minimum and maximum values of the graph are the minimum and maximum values of the metric data.


Metric Settings Page


Note that metric settings are also used when coloring a functional volume.

Current Selection Group

Shows the name, minimum value, and maximum value for the selected metric view and threshold data.  Pressing the Histogram Button will show a histogram of the view or threshold metric data.

Color Mapping Group

Determines the mapping of metric values to color in the color palette. 

Auto Scale   Maps the most positive view metric value to the 1.0 color in the color palette, the most negative view metric value to the -1.0 color in the color palette, and zero in the view metric to the zero color in the color palette.  If multiple metric columns are displayed while this color mapping is selected, identical colors will likely map to different metric values.

Auto Scale - Percentage  All of the positive values are sorted, all of the negative values are sorted, and all zero values are ignored.  The metric value that is at the "Pos Min Percentage" from the smallest positive value is mapped to zero in the color palette.  The metric value that is at the "Pos Max Percentage" from the smallest positive value is mapped to 1.0 in the color palette.  Negative values are processed in the same manner.  Unless these "Pos Min" and "Neg Min" values are very, very close to zero, you will see differences in this coloring mode compared to when auto scale is used.

Auto Scale - Metric Column   Maps the palette 1.0 color to this item's selected metric column's maximum value.  The palette's -1.0 color is mapped to this item's selected metric column's most negative value.  If multiple metric columns are displayed, using this colror mapping results in identical metric values mapping to identical colors.

Auto Scale - Functional Volume function is similar to the Auto Scale - Metric execept that the currently selected functional volume is used instead of the view metric data. 

User Scale allows the user to specify the positive view metric value (Pos Max) that maps to the 1.0 color in the palette, the positive view metric value (Pos Min) that maps to zero in the palette, the negative view metric value (Neg Max) that maps to the -1.0 color in the palette, and the negative view metric value (Neg Min) that maps to the zero color in the palette.

Interpolate Check Box  If checked, a nodes metric coloring is interpolated from the two colors that the metric value falls within in the color palette.  If unchecked, no interpolation is performed and discrete bands will be seen in the node's metric coloring.

Display Mode


Positive  Limits display to metric values greater than or equal to zero.

Negative Limits display to metric values less than or equalt to zero.

Both  Places no limits on the display of metric values.

Palette


Allows selection of the available color palettes that are used to color metric data.  Palettes may be created and edited by selecting Edit from the Attributes->Palette menu.

Display Color Bar  If checked, the color palette is displayed in the lower right corner of the main window.

Threshold


Thresholding allows the user to eliminate from display metric values between zero and the specified value using the selected Metric Threshold column.  Typically, the thesholding is set to a statistical significance. 

Column - These values are stored in the metric file for each column and are the values entered when mapping a volume using the Attributes->Map Volume(s) to Surface(s) Dialog.

Avg Area  - These values are stored in the metric file for each column and are a result of the values entered when mapping a volume using the Attributes->Map Volume(s) to Surface(s) Dialog and using Multi-Fiducial Mapping (MFM).  When mapping using MFM, the volume is mapped onto each of the twelve surfaces and then the average of these twelve mappings is computed and stored in a metric column.  For each of the twelve surfaces, a count of the number of nodes exceeding each of the positive and negative thresholds is found and then an average of these counts is deteremined.  The MFM metric column is sorted and the Avg Area threshold is set to the value of the node at the "average count" index from the maximum and minimum values.

User - These values may be entered by the user and are neither stored in the metric file nor change when the selected metric column is changed.

Show Subthresh Region Green  If checked nodes failing a threshold test are shown in a blue-like green for positive values and negative values for an olive-like green for negative values.

Threshold Type - Selects the type of thresholding (Column, Avg Area, or User) that should be applied.


Metric Selection Page


This page allows selection of the viewing column, the threshold column, comment ("?"), metadata ("M"), and histogram ("H") for each column.  In addtion, this page allows editing of the column names.

Models Main Page

This page controls the display of VTK model files which are shown in windows containing fiducial surfaces.  A transform (created using the Transformation Matrix Editor from the Windows Menu) may be used to control the location and orientatino of the model

Models Settings Page


Show Polygons  Enables the display of polygons (more than 3 vertices) in the displayed VTK models.

Show Triangles  Enables the display of triangles in the displayed VTK models.  If the VTK model was generated by caret, this enables the display of the surface.

Show Lines  Enables the display of lines in the displayed VTK models.

Show Vertices  Enables the display of vertices (points) in the displayed VTK models.  If the VTK model was generated by caret as a solid structure, this enables the display of the model's internal structure.

Opacity
  Controls the opacity of the models.

Line Size  Controls the width of lines in the displayed models.

Vertex Size  Controls the size of vertices in the displayed models.

Light Lines  Enables lighting when lines are drawn.

Light Polygons  Enables lighting when polygons are drawn.

Light Vertices  Enables lighting when vertices are drawn.


Paint Main Page


Geography Blending  - This control adjust the geography blending value that is used when geography blending is one of the base overlays.

Medial Wall Override Group


Enable Medial Wall Override  If this option is selected, and the paint file column selected immediately below this option contains nodes named "MEDIAL.WALL", those nodes will be painted with the MEDIAL.WALL color and override all other coloring.  This option is provided to "gray-out" the medial wall on surfaces using a closed topology file and hence prevent showing functional activations in the medial wall.

Display Color Key  Displays a color key for the selected paint column.

Paint Column Page



This page page is used to select a paint column for display, view the paint column's comment ("?"), view the metadata ("M"), and edit the name of a paint column.

Paint Name Page


This page allows the selection of individual paint names for display.

Probabilistic Atlas Surface Main Page

Display Mode   Normal blends the colors for all selected channels when coloring a node.  Threshold colors a node when at least "Threshold Ratio" of the selected channels match (have the same label).

Treat name "???" as if it was name "Unassigned"  If checked any nodes that have the label "???" which means no assignment are treated as if the label was "Unassigned".

Threshold Ratio  Use when the Display Mode is Threshold.  The percentage of a node's channels that must have the same value for a probabilistic color to be displayed on the node.

Display Color Key  Display a color key for the probabilistic atlas.


Probabilistic Atlas Surface Channels Page


Allows control over which channels (column) are used for probabilistic atlas surface coloring.

Probabilistic Atlas Surface Areas Page


Allows control over which labels (paint names) are used for probabilistic atlas surface coloring.

Probabilistic Atlas Volume Main Page

Display Mode   Normal blends the colors for all selected channels when coloring a voxel.  Threshold colors a voxel when at least "Threshold Ratio" of the selected channels match (have the same label).

Treat name "???" as if it was name "Unassigned"  If checked any voxels that have the label "???", which means no assignment, are treated as if the label was "Unassigned".

Threshold Ratio  Use then the Display Mode is Threshold.  The percentage of a voxel's channels that must have the same value for a probabilistic color to be displayed on the voxel.


Probabilistic Atlas Volume Channels Page


Allows control over which channels are used for probabilistic atlas volume coloring.

Probabilistic Atlas Volume Areas Page


Allows control over which labels are used for probabilistic atlas volume coloring.


Region Page


Used with Washington University Region files.


RGB Paint Page


RGB Paint File Group 


This section allows the user to control of the RGB data.  The checkboxes control the display of the red, green, and blue channels.  The thresholds are used to inhibit display of data below the thresholds and he thresholds should always be positive. 

Display Mode

Positive Only  Only positive values are shown and the maximum positive value is mapped to the full intensity of its corresponding color.

Negative Only  Only negative values are shown and the maximum positive value is mapped to the full intensity of its corresponding color.

Scene Page


At the of the scene page is a list box containing a list of the available scenes.  A scene must be selected for some of the buttons to function correctly.  Some of the buttons will operate when multiple scenes are selected.  To select a contiguous group of scenes, click the mouse on the first scene and then shift-click the mouse on the last scene.  To select a non-contiguous set of scenes, click the mouse on the first scene and then control-click (Apple-click on Macs) on additional scenes.

Show Selected Scene  Press this button to show the selected scene.  A scene may also be displayed by double-clicking its name in the list box.

Append New Scene  Press this button to create a new scene that becomes the last scene in the list box.

Insert New Scene  Press this button to create a new scene and insert it below the currently selected scene.

Replace Selected Scene  Press this button to create a new scene and replace the currently selected scene.

Delete Selected Scene  Press this button to delete the selected scene.

Check All Scenes   Press this button to test all scenes and display any errors encounted after showing the last scene.

Unload All Files Except Scene   Remove all data files from memory except the scene file.

Create Spec From Selected Scene  Create a spec file using all of the files in the selected scenes.

Transfer Identity Window Filters   Pressing this button allows the user to choose a scene and then the Identity Window Filters are transferred from this scene to all of the scenes selected on the Display Control's scene page.

Window Positioning 

Use All Window Positions From Scene  The main window and all other windows are place in the scene's reported location.  The problem with using this option is that monitor size can vary and the windows may be mostly off the screen if the scene is displayed on a computer with a smaller monitor than was used to create the scene.  Caret will prevent windows from being completely off the screen.

Do Not Move Main Window, All Other Windows Relative to Main Window  When displaying the scene, do not alter the Main Window's current position.  Place other windows at a position relative to the offset of the window's location from the main window in the scene.

Ignore All Window Positions in Scene  Do not alter the positions of any of the user's windows.


Section Page


The control adusts the sections visible when sections are one of the overlays.

Surface Shape Selection Page


This page is used to select a shape column for display, view meta-data for a column using the "?" button, and changing the names of shape columns.

Surface Shape Setttings Page

Selected Column Group


This group shows the minimum and maximum values for the currently selected Surface Shape column.  Mapping lists the Surface Shape value that is mapped to least intensity (such as black) and greatest intensity (such as white).  Pressing the Histogram button will popup a window showing the distribution of values for the currently selected Surface Shape column. 

Color Mapping Group


Gray  Colors the surface shape data with white at the Mapping maximum and black at the Mapping minimum.

Orange-Yellow  Colors the surface shape data with bright yellow at Mapping maximum and dark orange at Mapping minimum.

Palette  Colors the surface shape data with a palette from the Palette File.

Interpolate Palette Colors  Provides a smooth shading when coloring the surface shape data using a Palette.

Display Color Bar  Displays the palette color bar in the lower left corner of the Main Window.

Node ID Deviation  If checked and a node is identified, the node identification symbol will be a sphere where the sphere's radius obtained from the column selected in the Node ID Deviation box.


Surface and Volume Page


This page controls the display of data on a Surface & Volume brain model.

Surface Group


Show Surface   Shows the active fiducial surface in the Surface & Volume brain model.  The active fiducial surface is selected on the Surface Miscellaneous page.

Anatomy Volume Group


Horizontal Slice  Enables the horizontal slice for display and controls the selected horizontal slice.

Parasagittal Slice  Enables the horizontal slice for display and controls the selected parasagittal slice.

Coronal Slice  Enables the horizontal slice for display and controls the selected coronal slice.

Volume Overlays Group


Show Primary Overlay  Displays the selected Primary Overlay on the volume slices.

Show Secondary Overlay  Displays the selected Secondary Overlay on the volume slices.

Functional Volume Group


Show Volume Cloud   Displays the selected functional volume voxels in 3D which may be slow to render.

Opacity  Enable opacity for the functional volume cloud.

Segmentation Volume Group


Show Volume Cloud  Shows the selected segmentation volume's voxels in 3D which may be slow to render.

Vector Volume Group


Show Volume Cloud  Shows the selected vector volume's voxels in 3D which may be slow to render.

Surface Clipping Page


Surface clipping allows one to remove parts of a displayed surface.

Apply Clipping  Determines which surfaces are clipped.

Negative X  Removes everything with an X-coordinate less than this value.

Positive X  Removes everything with an X-coordinate greater than this value.

Negative Y  Removes everything with an Y-coordinate less than this value.

Positive Y  Removes everything with an Y-coordinate greater than this value.

Negative Z  Removes everything with an Z-coordinate less than this value.

Positive Z  Removes everything with an Z-coordinate greater than this value.

Surface Miscellaneous Page


Left Fiducial Volume Interaction   Fiducial surface used for surface and volume interaction with the left cerebral cortex.

Right Fiducial Volume Interaction
   Fiducial surface used for surface and volume interaction with the right cerebral cortex.

Cerebellum Fiducial Volume Interaction   Fiducial surface used for surface and volume interaction with the cerebellar cerebral cortex.

Active Fiducial  Select the fiducial surface that functions as the "active fiducial" surface.  The active fiducial surface is used in Surface & Volume view and other instances.

Drawing Mode   Determines the method used to draw the surface.
Projection  Switches between orthographic and projective viewing.  With projective viewing, objects (of the same size) appear smaller the further they are from the viewing.  With orthographic viewing objects do not appear to be smaller as they move away from the viewer.

Brightness Adjusts the brightness of the surface.  The brightiness value is added to the red, green, and blue color components.

Contrast   Adjusts the contrast of the surface.  The red, green, and blue color components are multiplied by the contrast value.

Opacity  Adjust the transparency of the surface.  Opaque is 1.0 and fully transparent is 0.0.  The drawing mode Tiles with Lighting No Backfacing may be helpful when the surface is transparent.

Node Size  The size of node symbols (in pixels) when the surface is drawn as nodes.

Link Size  The width of the links (in pixels) when the surface is drawn as links.

Identify Color  The color of the symbols displayed when a node is identified.

Show Normals  Shows the normals as small vectors attached to the surface nodes.

Show Morphing Total Forces  Shows the morphing total force as small vectors attached to the nodes.

Show Morphing Angular Forces  Shows the morphing angular force as small vectors attached to the nodes.

Show Morphing Linear Forces  Shows the morphing linear force as small vectors attached to the nodes.

Force Vector Length Exaggerates the lengths of the morping force vectors.

Surface Cartesian Axes Display cartesian axes with the surface.

Show Orientation Labels  Shows labels (X, Y, Z) at the ends of the axes.

Show Tick Marks Shows tick marks every 10mm on the axes.

Axes Length The length of the axes.

Axes Offset Offset of the axes from the origin.

Topography Page


The popup menu selects a column from the topography file.

Display Mode Group


Eccentricity  Shows the eccentricity data from the selected topography file column.

Polar Angle  Shows the polar angle data from the selected topography file column.


Vector Selection Page



Vector Settings Page

Coloring Mode  Determines method for colorization of vectors.
Drawing Mode Controls how the vectors are drawn. 
Display Mode Surface  Controls the display of vectors with fiducial surfaces (vectors are only displayed with fiducial surfaces since the vectors are not associated with surfaced node).  All displays all vectors, Sparse shows a subset of vectors, and  None inhibits the display of all vectors.

Display Mode Volume  Controls the display of vectors on volume slices.  All displays all vectors, Sparse shows a subset of vectors, and  None inhibits the display of all vectors.

Orientation  Controls the display of vectors to those that are directed along one of the standard axis.

Orientation Angle  The maximum angle between a vector and a standard axis (selected Orientation) that allows display of the vector.

Functional Mask  Allows selection of a functional volume that is used as a mask for the display of vectors. 

Functional Neg/Pos Threshold  If a functional mask is enabled, vectors are only displayed if the voxel containing the origin of the vector has a value less than the negative theshold or greater than the positive threshold.

Segmentation Mask  If enabled and a segmentation volume is selected, only vectors with an origin inside of a non-zero voxel in the segmentation volume are displayed.

Sparse Distance Skip  Controls the number of indices that are skipped when the Display Mode is Sparse.

Length Multiplier   Exaggerates the length of the vectors by multiplying the vector magnitudes by this amount.

Magnitude Threshold  Vectors with a magnitude less than this value are not displayed.

Surface Line Width  Controls the width of lines when vectors are displayed on the surface as 2D lines.

Volume Slice Above Limit  When drawing vectors on volume slices, only vectors whose distance above the slice is less than this value are displayed.

Volume Slice Below Limit  When drawing vectors on volume slices, only vectors whose distance below the slice is less than this value are displayed.

Draw With Magnitude  If selected, the length of the drawn vector reflects the vector's magnitude.  If not selected, the vector is drawn as a unit vector (length is 1.0).

If some of the vectors are "under" the surface, try adjusting the Surface Opacity on the Surface Miscellaneous page.

Volume Settings Page


Anatomy Volume Group


Draw Type  Controls the coloring of anatomy volumes.   0 to 255 maps 0 to black and 255 to white.  Min to Max maps the minimum value in the volume to black and the maximum value in the volume to white.  2% to 98% first sorts the voxel values and then maps the value that is 2% of the total number of voxels from the minimum value to black and the voxel that is 2% of the total number of voxels from the maximum value to white.

Brightness is used to adjust the brightness of the anatomy volume.

Contrast is used to adjust the contrast of the anatomy volume.

Make Default  Pressing this button sets the default brightness and contrast to the current brightness and contrast.

Histogram  Shows a histogram of the anatomy volume's voxels.

Oblique Slices Viewing Group


View Matrix  Chooses the matrix that controls oblique volume viewing.

Slices Sampling  Chooses the sampling that is performed when viewing a volume obliquely.  Smaller values may remove "blockiness" but may slow interaction, such as rotating, with the volume.


Functional Volume Group


Display Color Bar   Shows how the voxel values are mapped into the color palette.  Note that Functional Volumes are colored using the Metric selections.

Segmentation Volume Group


These controls affect the coloring of segmentation voxels.   Translucent allows the underlay (typically anatomy voxels) to show through the segmentation voxels to simultaneously visualize the segmentation and the anatomy.  Opaque overrides any underlay coloring.  Outline draws the segmentation voxels as outlined (open) rectangles.  Cross draws the segmentation voxels as crosses (similar to "+").

Translucency is used in the Translucent mode to adjust the translucency of a segmentation voxel.  (translucency * segmentation voxel + (1.0 - translucency * underlay voxel).

Montage Group


When checked, shows a grid of slices for volume viewing.

Rows  Controls the number rows for the montage slice viewing

Columns  Controls the number of columns for the montage slice viewing

Increment  Controls the increment in slices for each slice viewing in montage viewing.

Overlay Opacity Group


Controls the opacity for the overlay when a voxels is (opacity * overlay-color + (1.0 - opacity) * underlay-color).


Color Keys Group


Paint Color Key  Shows the color key for the selected paint volume.

Prob Atlas Color Key  Shows the color key for the probabilistic atlas volumes.

Animation Group


Start  Starts animating through the slices displayed.

Stop  Stops animating throught the slices displayed.

Direction  Controls whether animation slices are increased (positive) or decreased (negative).


Crosshairs Group


Show Crosshairs  Shows crosshairs that intersect at the last identified location.

Show Crosshair Coordinates  Shows the stereotaxic coordinates of the crosshair intersection in the bottom, left corner of the window.


Vector Volume Group


Sparsity  Draws vectors for every "X" voxels.


Volume Surface Outline


Enables the display of up to surface outlines over the volume slices and may be helpful to verify that a volume and it corresponding surface are in the same stereotaxic space or the quality of the surface reconstruction.  This is unlikely to work if surfaces other than a raw or fiducial surface are selected.