Caret6:Documentation/UserInterface/SurfaceRegionOfInterestOperationsWindow

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Surface Region of Interest Operations Window

This window is used for selection of and operations on regions of interest (ROI).

Selection Page

Structure and Surface Selection

  • Structure - Selects the structure used for node selection and operations.
  • Surface - Surface used for node selection and operations.

Region of Interest Selection

Each structure maintains a region of interest file that contains one or more regions of interest.

  • Region Combo Box - Use to select a region of interest for processing.
  • Add - Press to add a new region of interest.
  • Rename - Press to rename the selected region of interest.
  • Delete - Delete's the selected region of interest.

Node Selection

  • Source - Selects the source (data type) used for node selection.
    • All Nodes - All connected nodes are selected.
    • Borders - Nodes within a border on the flat surface are selected.
    • Labels - Nodes with a specific label are selected.
    • Metric - Nodes with a range of metric values are selected.
    • Shape - Nodes with a range of shape values are selected.
  • Select Nodes - Pressing this button selects nodes using the selected Source.
  • Logic - The logic determines how newly selected nodes are combined with any previously selected nodes.
    • Normal - Any previously selected nodes are deselected after which new nodes are selected using the current source.
    • And (Intersection) - The selected nodes are those that are selected using the current node selection source AND were previously selected.
    • Or (Union) - The selected nodes are those that are selected using the current node selection source OR were previously selected.
    • And Not - The selected nodes are those that are selected using the current node selection source AND WERE NOT previously selected.
  • Show Selected Nodes - If this is checked, the selected node are displayed in green. To the right of this control is the number of nodes that are currently selected.

Border Options

This panel is displayed when the Source is Borders.

  • Flat Surface - The flat surface used to determine which nodes are inside a border.
  • Border Name - Name of the border that is selected.
  • Select Name from List - Pops-up a dialog for selecting a border name.
  • Select Border Using Mouse - Sets the mouse is used to select a border and the border's name is entered in the Border Name text box.

Label Options

This panel is displayed when the Source is Label File.

  • Column - Selects the data column used for selecting labels.
  • Label Name - Name of label that is selected.
  • Select Name from List - Pops-up a dialog for selecting a label name.
  • Select Name Using Mouse - Sets the mouse is used to select a node and the node's label name is entered in the Label Name text box.

Metric Options

This panel is displayed when the Source is Metric File.

Metric File Options

  • Column - Metric file column used for node selection.
  • Maximum - Maximum metric value of nodes that are selected.
  • Minimum - Minimum metric value of nodes that are selected.

Metric File Node Selection Method

  • All Nodes Within Range - Allows selection of all nodes that have a metric value within the range of values.
  • Nodes Within Range Connected to Node Number X With Value - Allows the user to select a node and the selection is limited to those nodes that are connected to the selected node and within the range of values. To enable the mouse for node selection, select or re-select this radio button.

Shape Options

This panel is displayed when the Source is Shape File.

Shape File Options

  • Column - Shape file column used for node selection.
  • Maximum - Maximum metric value of nodes that are selected.
  • Minimum - Minimum metric value of nodes that are selected.

Shape File Node Selection Method

  • All Nodes Within Range - Allows selection of all nodes that have a shape value within the range of values.
  • Nodes Within Range Connected to Node Number X With Value - Allows the user to select a node and the selection is limited to those nodes that are connected to the selected node and within the range of values. To enable the mouse for node selection, select or re-select this radio button.


ROI Modification

  • Deselect All - Deselects all nodes.
  • Dilate - Adds a layer to all selected regions.
  • Erode - Removes a layer from all selected regions.
  • Extent - Limits the selected nodes to a three-dimensional box.
  • Invert - Inverts the selected nodes.
  • Remove Islands - Deselects node excepts those in the largest connected region.

Operations Page

Operation Selection - Use this control to select the operation that is performed using the surface region of interest.

All operations take place using the structure and surface selected on the Selection page of this dialog.

Press the Run Operation button at the bottom of the dialog to perform the selected operation.

Assign Labels

Selected nodes are assigned a label in the selected label file column.

  • Label File Column - Press this button to create a new column in the label file. Use the control on the right to choose an existing column in the label file.
  • Label Name - Press this button to choose an existing label or a name from other data sources. Or, simply enter the name of the label in the text box on the right.

Assign Metric

Selected nodes are assigned a metric value in the selected metric file column.

  • Metric File Column - Press this button to create a new column in the metric file. Use the control on the right to choose an existing column in the metric file.
  • Value - Enter the value that is assigned to the nodes.

Assign Shape

Selected nodes are assigned a shape value in the selected shape file column.

  • Shape File Column - Press this button to create a new column in the shape file. Use the control on the right to choose an existing column in the shape file.
  • Value - Enter the value that is assigned to the nodes.

Folding Measurements Report

Creates a report that reports a variety of folding measurements on the selected surface.

  • Create Metric File - If this control is checked a metric files is written that contains folding measurements for all nodes.

Statistical Report

Creates a report with statistical measurements of label, metric, and shape data on the region of interest.

  • Metric Distortion Column - If selected, a metric column may be designated as containing surface distortion. This is typically used with an averaged surface and adjusts the surface area of nodes so that they approximate the surface area of an individual.
  • Separate Report with Semicolons - Places semicolons in the report so that the results may be imported into a spreadsheet.

Create Volume ROI from Surface ROI

Creates a segmentation volume by intersection the surface region of interest with the volume.

A surface is infinitely thin. To approximate the thickness of the cerebral cortex, the surface is shrunk and expanded to approximate the thickness of the surface.

  • Segmentation Volume - Press this button to create a new segmentation volume. Use the control on the right to select an existing segmentation volume.
  • Inner Boundary - Amount surface is shrunk during intersection with the volume.
  • Outer Boundary - Amount surface is expanded during intersection with the volume.
  • Thickness Step - Amount surface changes in size as it is expanded from inner boundary to outer boundary.
  • Clear All Voxels - If selected, all voxels are set to zero in the selected volume prior to intersection. Deselection of this option allows one to combine multiple intersections into a single volume.
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