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
- Areal Estimation
Similar to a paint file but uses uncertainty that is shown by fuzzy
instead of abrupt boundaries.
- CoCoMac (Collations of
Connectivity Data on the Macaque Brain, www.cocomac.org).
When a node is selected, the selected paint area is shown in red and
other paint areas with known connections are shown in green.
- Metric Typically
used for the display of functional data but is nothing more than a
floating point number at each node.
- Paint Labels
identifying nodes in the surface.
- Probabilistic Atlas
Colors
the surface in a probabilistic fashion. The probabilistic atlas
file is the same as a paint file, except that each column in a
probabilistic atlas file contains the same type of data (such as sulcal
identification) but from different subjects.
- RGB Red, Green,
Blue coloring applied to the surface's nodes.
- Shape Typically
used for surface shape data such as curvature and depth. The same
file format and interchangible with metric data.
- Topography Polar
angle and eccentricity for visual areas.
- Crossovers Shows
nodes in red that are identfied as being parts of crossovers.
- Sections Shows
sections in blue. A value of "10" shows section 10 in blue
whereas a value of "10X" shows every 10th section in blue.
- Edges Shows edge
node in blue.
- Geography Blending
Uses the
Paint File's column named "Geography" to darken the overlay coloring of
nodes that are identified as SUL (sulci).
Coloring Mode
- NORMAL Traditional
coloring where the underlay is applied first, followed by the overlays.
- BLEND OVERLAYS
Applies the Underlay first and then applies a blend of the three
overlays.
Layers
- Borders - Enables the
display of borders.
- Cells - Enables the
display of cells.
- Foci - Enables the
display of activation foci.
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.
- Nodes draws each node as
a point.
- Links draws the links as
line segments.
- Links (No Backside) draws
the the links as line segments but does not allow the user to
"see-through"
the surface.
- Links (Edges Only) draws
the links as line segments but only those links that are edges (such as
those in cut topology). If there are no cuts in the surface,
nothing will be displayed.
- Nodes and Links draws the
surface as both nodes and links.
- Tiles draws the surface
as shaded triangles.
- Tiles with Lighting
Draw the surface as shaded triangles with lighting (default drawing
mode).
- Tiles with Lighting No Backfacing
Tiles Draws the surface as shaded triangles with lighting but parts of
the surface that face away from the viewer are not drawn. This
should provide better performance than Tiles with Lighting. It is
also useful if surface opacity is less than one so that the "other
side" of the surface is not displayed.
- Tiles, Links, and Nodes (surface
editing) draws the surface as tiles, links, and nodes and
is typically used when editing a flat surface's nodes and links.
- Hide Surface
Nothing is drawn.
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.
- Use Vector Colors
Vectors are colored with the colors associated with each vector in the
vector file.
- Use XYZ as Red, Green, Blue
Vectors are colored using the unit vector as color components.
The X-component is assigned to red, the Y-component is assigned to
green, and the Z-component is assigned to blue.
Drawing Mode Controls how the
vectors are drawn.
- Directional (3D Arrows on
Surface) Draws 3D arrows on the surface
and 2D arrows on the volume. Surface drawing may be very slow if
there are many vectors.
- Oriented (3D Cylinders on
Surface) Draws 3D cylinders with the
center of the cylinder at the vector's origin.
- Directional (2D Lines with End
Points on Surface) Draws lines
with a point on the tip on the surface and on the volume.
- Oriented (2D Lines on Surface)
Draws lines on the surface and on
the volume with the center of the line at the vector's origin.
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.