Caret6:Documentation/UserInterface/FociOperationsWindow

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Contents

Foci Operations Window

Toolbar

  • DA - Delete all foci.
  • DN - Delete non-displayed foci.
  • DF - Delete foci clicked with left mouse button.

Add, Delete, and Edit Foci Page

Focus Selection

  • Focus Number - Use this control to select a focus for editing.
  • First - Selects the first focus in the currently loaded foci projection file.
  • Last - Selects the last focus in the currently loaded foci projection file.

File Operations

  • Add New Focus - Press this button to add a new focus. The new focus may be either a copy of the currently selected focus or a new focus with all data fields empty.

Focus Operations

  • Delete Focus - Press this button to delete the selected focus.

Focus Data

  • Name - Name of focus.
  • Coordinate - Stereotaxic coordinate of the focus. If the coordinate is changed the Apply button must be pressed to update the graphics windows.
  • Area - Cortical Area of the focus.
  • Class - Class of the focus. You can make up classes to group foci by their class names. Use the Display Control Dialog's Foci Class page to control the display of foci by their class name.
  • Extent - Size of the focus.
  • Geography - The geographic name corresponding to the location of the focus.
  • Region of Interest - A region-of-interest relating to the focus.
  • Study Metadata - Set a link or links to Study Metadata.
  • Statistic - The type of statistic associated with a focus.
  • Comment - Additional description of the focus.

Attribute Assignment Page

Surface Selection

When foci attributes are assigned with labels, the label's source is the node found nearest to the focus using these surfaces. The original stereotaxic coordinate is used for the spatial location of the focus. If the node nearest the focus is more than "Maximum Distance from Surface" units (millimeters) from the focus, no assignment is made to the focus.

Attribute Assignment

  • Assign to
    • All Foci - Attributes assignments are made to ALL foci.
    • Displayed Foci - Attributes are assigned only to foci that are displayed on any surface.
  • Assignment Method
    • Append - Any new attributes are appended to current attributes of the focus. Multiple attributes are separated by a semi-colon.
    • Clear - The attribute is cleared (set to empty text).
    • Replace - The attribute is cleared and then any new attributes are assigned.
  • Assign Focus Attribute
    • Area - Assigns the focus' Area attribute.
    • Class - Assigns the focus' Class attribute.
    • Geography - Assigns the focus' Geography attribute.
    • Region of Interest - Assigns the focus' Region of Interest attribute.

Assign Foci Attributes With

  • Text - Assigns the text in the text box to the focus attribute.
  • Labels Assigned to Closest Node - If there are any label files loaded, the names of the label columns are listed with checkboxes for selection. The checked label columns are used for the attributes assigned to the focus.

Edit Foci Colors Page

Use this page to edit the foci colors.

Color Names

This section contains a list of the current foci colors. To edit a foci color, simply click the name of the foci color and modify the color's components in the Color Component Editing section.

  • New Color Button - Press this to enter a new color name.
  • Change Name - Changes the name of the currently selected color.
  • Delete Selected Color - Press this button to delete the selected color.

Color Component Editing

A the top of this section is an alternating black and white pattern. For opaque colors (Alpha = 255) this pattern is not seen. As the Alpha value is reduced, this black and white pattern appears. Its purpose is to provide feedback for transparent colors (those with Alpha less than 255).

  • Name - Name of the currently edit color.
  • Red - The red color component.
  • Green - The green color component.
  • Blue - The blue color component.
  • Alpha - The alpha (transparency) color component.

Advanced - Pressing this button provides other user-interface components for setting a color's components.


Miscellaneous

Delete Unused Colors - Removes any colors that are not assigned to a focus.

Foci Projection To Atlas

Atlas Selection

Selects the atlas to which the foci are mapped.

Map to Structures

Selects the structures to which foci are projected. The list of available structures will vary based upon the structures in the atlas.

Cerebral/Cerebellar Projection

Some foci are spatially located in a location that is ambiguous as to the associated structure, cerebral hemisphere or cerebellum.

Cerebral Cutoff (R1) - Determines the associated structure of the focus when spatial location is ambiguous to the cerebral cortex and the cerebellum (see below). Cerebellum Cutoff (R2) - Determines the associated structure of the focus when spatial location is ambiguous to the cerebral cortex and the cerebellum (see below).

  1. A ratio of distance to cerebral cortex divided by distance to cerebellum is computed.
  2. If this ratio is less than Cerebral Cutoff (R1), the focus is assigned to the cerebral cortex.
  3. If this ratio is greater than Cerebellum Cutoff (R2), the focus is assigned to the cerebellum.
  4. If the ratio is between the two cutoffs, the focus is projected to both the cerebral cortex and the cerebellum.

Spatial Projection Type

  • Project Above Surface - If selected, each focus is projected and its position is set so that it is the specified distance above the surface. When the distance is zero, foci are placed directly on the surface. If the distance is negative, the foci will be under the surface and not visible unless the surface opacity is adjusted.
  • Normal Projection - The focus maintains its accurate distance in relation to the surface (and possibly under the surface).

Foci Projection to Surfaces Page

Press the Apply button to project the foci. By projecting foci, the foci are visible on surfaces other than the anatomical surface in a position relative to the surfaces.

Projection Surfaces

Use this section to select the surfaces for the projection of foci.

Spatial Projection Type

  • Project Above Surface - If selected, each focus is projected and its position is set so that it is the specified distance above the surface. When the distance is zero, foci are placed directly on the surface. If the distance is negative, the foci will be under the surface and not visible unless the surface opacity is adjusted.
  • Normal Projection - The focus maintains its accurate distance in relation to the surface (and possibly under the surface).

Unproject Foci Page

Unprojection Destination

  • Unproject to Original XYZ - Unprojects the foci replacing their original coordinates. The original coordinates are the reported location of the activation so use this selection with caution.
  • Unproject to Volume XYZ - Unprojects the foci to the volume coordinates so that the foci may be viewed on volume slices.

Unprojection Surfaces

This section allows selection of surfaces for unprojection of foci.

Options

  • Paste Onto Surface - Unprojects the foci so that they are directory on the surfaces with no offset.


Foci Report Page

This page generates a report of foci attributes. The report is displayed in a spreadsheet-like layout. The widths of columns is adjusted by manipulating the column title headers. To sort by any column, simply click the column title. Click the column title a second time to reverse the ordering.

Structures/Surfaces

Selects the surface for each loaded structure.

Data Attributes

Selects the attributes that are included in the report.

Label Attributes

If there are label files loaded, this section is displayed. If any label column names are selected in this section, the, for each focus, its nearest node is determined and the label(s) from that node are placed in the foci report.

Options

  • Show Only Displayed Foci - If selected, the report includes just the foci that are displayed.
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