Surface Region Of Interest Dialog
Region of Interest Node Section
This section of the dialog is used to select nodes that make up the
region of interest. There are several different methods used to
After setting the options that determine how nodes are selected, the
user must press the "Select Nodes" button to actually select
the nodes. Unless "Show Selected Nodes" is unchecked, the
selected nodes will
be shown in green. In addition, the number of nodes selected will
shown on the dialog.
- Entire Surface - This will select all nodes in the surface.
- Nodes With Paint - This selects nodes that have been
assigned a name in the specified paint category. First, select
the category (paint
column name). Next, there are two ways to select the paint name.
"Select Name From List" button pops up a dialog that allows the paint
to be selected from a list. The "Select Node With Mouse" button
the mouse into a mode so that the user can click a node on the surface
the paint name assigned to that node will be used.
- Nodes Within Border - This selects nodes that are within a
closed border on a flat surface. The "Select Name From List"
allows the user to select the name of the border. The "Select
Border With Mouse" allows the user to select a border by clicking on it
with a mouse. The "Flat Surface" combo box allows the user to
select the flat surface that is used for testing nodes within the
- Nodes Within Lat/Long Range
- Selects nodes whose latitude and longitude values are within a
- Nodes With Metric - This select nodes based upon the
nodes' currently displayed metric values. First, the user enters
the lower and upper thresholds that limit the nodes selected to those
with a displayed metric within the thresholds. Next, there are
two ways to control how the nodes are selected. "All Nodes Within
Threshold" will select all nodes on the surface whose displayed metric
value is within the threshold. "Nodes Within Threshold Connected
to Nodes Selected With Mouse" only selects nodes that are connected to
the node selected with the mouse and within
- Nodes With Surface Shape
- Like Nodes With Metric but selects nodes based upon their surface
- Nodes With Crossovers -
Selects nodes that have been identified as crossovers. Crossovers
are identified using Surface Menu->Measurements->Crossover Check.
There are several options to combine nodes newly selected with
previously selected nodes when the "Select Nodes" button is pressed:
- Normal Selection - In this mode, all previously selected
nodes are deselected prior to performing the new selection.
- And Selection (Intersection) - In this mode, the new
selection is made but only nodes that were previously selected and
selected by the current selection method remain selected.
- Or Selection (Union) - In this mode, the new
is made and all nodes from the current selection and nodes that were
previously selected remain selected.
- Not Selection - In this mode, only nodes that did not meet
the current selection criteria remain selected.
Operation Surface and Topology
This section selects the Surface on which the query will be performed.
It will also show the topology file that the surface is assigned.
topology can be changed by selecting "Set Topology" from the Surface
Operate on Selected Nodes
There several different operations that are performed on the selected
- Assign Metric Column for
Selected Nodes - Sets the metric value all of the nodes in the
region of interest to the "New Value".
- Assign Paint Attributes to Selected Nodes - This will
assign the paint name for the selected nodes to an existing or new
paint column when
the "Assign Paint" button is pressed.
- Assign Surface Shape Column for
Selected Nodes - Sets the surface shape value all of the nodes
in the region of interest to the "New Value".
- Compute Integrated Folding Index
- The average folding index is SUM(Ai * ABS(Fi)) / SUM(Ai). Ai is
the area of a triangle, Fi is the average shape value of the triangle's
three nodes, and
- Create Borders Around Clusters
- Creates borders around clusters in the ROI. The algorithm is
unable to create borders around very small clusters and those clusters
that contain a "bow-tie" (part of a cluster that has two triangles
connected by a single vertex).
- Create Open (Linear) Border From
ROI - The purpose of this operation is to automatically draw a
border along the fundus of a sulcus. First, set the selected
Surface Shape column on the Display Control's Overlay/Underlay -
Surface page to Folding (Mean Curvature). On this dialog, set the
Selection Method to Nodes with Surface Shape. Set the Low
Threshold to a very negative number, say -100000.0, and the High
Threshold to -0.10. Choose Nodes Within Threshold Connected to
Node Selected with Mouse, click the mouse over a dark area in the
fundus of the desired sulcus, and press the Select Nodes button.
This should result in selected node (green) symbols being placed over
the fundus the sulcus. It may be necessary to adjust the High
Threshold small amounts. In the Operation section, enter a name
for the border. Set the Starting and Ending Node Selection to
Manual. Press the Select with Mouse button in the Start Node row
and choose one of the highlighted nodes with the mouse where you would
like the border to start. Press the Select with Mouse button in
the End Node row and choose one of the highlighted nodes with the mouse
where you would like the border to end. Press the Create Border
Along Sulcus button to create the border. Automatic mode can be
used with borders that are fairly linear that have little or now
branches. Automatic mode attempts to determine the two nodes that
are furthest apart and creates a border between them.
- Create Volume ROI from Selected Nodes - This creates a
"segmentation" volume where voxels are set if the voxel intersects the
When the Create Volume from Displayed Query Nodes is selected, the Suface to Volume Dialog is
up. When viewing the volume, to help find the voxels that intersect the
"Show Voxel Dimensional Extent" from the Volume menu can be used.
- Disconnect Selected Nodes - Pressing the "Disconnect
Selected Nodes" will disconnect all selected nodes.
- Geodesic Distance - This will calculate geodesic distance
a node to all other nodes in the surface. The query node number
be entered or the "Choose Node With Mouse" pushbutton can be pressed
the query node selected with the mouse. Once a node is selected
the "Determine Geodesic Distances" pushbutton to calculate the geodesic
from the query node to all other nodes in the surface. The output
two columns added onto the current metric file. The first column
each node is its distance from the query node. The second column
the first node in the path from the node to the query node which may be
to show the path in a later update to Caret. The geodesic
is determined by a variant of Dijkstra's Shortest Path algorithm.
algorithm follows the links between nodes to find the shortest path
the query node to all other nodes. Use the default palette
for visualizing the metric column containing the node's distance from
- Probabilistic Atlas Overlap
Analysis - For each name in the probabilistic atlas file a
report is generated listing the count of nodes and percentages that use
the name 1 to M times where "M" is the number of columns in the
probabilistic atlas file.
- Smooth Selected Nodes - Allows smoothing of the selected
- Statistical Report on Selected Nodes - This creates a text
report (viewable on the "Report" tab) of various surface attributes
such as paint surface areas and statistical measurements of metrics and
- Statistic Report on Paint
Subregions - Produces a statistical report for each paint name
in the selected Paint Column.
- Surface Shape Correlation
Coefficient Report - Creates a matrix with each element
representing the correlation coefficient of each surface shape column
correlated to all other surface shape columns.
- Surface Shape Cluster Analysis
- Finds clusters of nodes based upon the nodes' surface shape values
that exceed the entered threshold. In the report, Threshold is
the threshold value used to find clusters, Column is the column in the
surface shape file (starting at one), Num-Nodes is the number of nodes
in the cluster, Area is the surface area of the cluster on the
Operation Surface, Area-Corrected is the corrected area on the
Operation Surface (see corrected area explanation later), COG-X, COG-Y,
and COG-Z are the X, Y, and Z coordinates of the center of gravity of
Using the PALS atlas average fiducial surface as the operational
surface may lead to inaccurate surface area calculations due to the
PALS average fiducial surface being an "average surface". If
there is a metric column selected on the Display Control Dialog, it is
used to adjust the surface area estimated at each node so that the
operational surface has a surface area near that of a normal cortex.
This page of the dialog allows the user to choose specifically what
metric, paint, and surface shape attributes are included in the
This page of the dialog contains the output of the statistical report.