Modules:Fiducials-Documentation-3.4

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Fiducials

Fiducials

List of Fiducial Points

Glyph Options

General Information

Module Type & Category

Type: Interactive

Category: Base

Authors, Collaborators & Contact

• Nicole Aucoin: Brigham and Women's Hospital
• Contact: Nicole Aucoin, nicole@bwh.harvard.edu

Module Description

The Fiducials Module creates and manages lists of Fiducial points.

Usage

New fiducials can be created in multiple ways:

• Click on the tool bar icon of an arrow pointing to a starburst fiducial to enter the 'place a new object mode', then use the mouse to left click on 3D models or on 2D slices to show where you wish to place your fiducials.

• You can also place fiducials while in 'tranform view' mode by positioning the mouse over a 2D slice plane in the Slice view windows (it must be the active window) and pressing the 'P' key.

• You can also add a new fiducial from the Fiducials module GUI, using the add button: [image:SlicerFiducialsAddNew.png]. This places a new fiducial at the origin, (0,0,0).

• You can right click and drag a fiducial in the 2D slice windows using the mouse in 'transform view' mode. 3D interactions are possible by clicking and dragging the fiducial glyph in the 3D window.

Quick Tour of Features and Use

List all the panels in your interface, their features, what they mean, and how to use them. For instance:

• Create and Select Fiducial Lists panel:

	Create and Select Fiducial Lists icons.
	Select all fiducial points from all lists.	Deselect all fiducial points from all lists.	Delete all fiducials lists and the fiducials they contain.
	Lock or unlock all fidicuial lists so that they cannot or can be moved in 3D.	Make all fiducial lists visible or invisible.

• Add, Configure and Delete Fiducials panel:

You can reset the positions of the fiducials in the table that appears in the Add, Configure and Delete section of the Fiducials GUI.

	Add, Configure, & Delete Fiducials icons.
	Add a fiducial point to the current fiducial list, at (0,0,0).	Select all fiducial points from this fiducial list.	Deselect all fiducial points from this fiducial list.	Delete the last fiducial that was clicked on in the table.	Delete all fiducial points from this fiducial list.
	Move last clicked fiducial up one in the list.	Move last clicked fiducial down one in the list.	Lock or unlock all fidicuial lists so that they cannot or can be moved in 3D.	Make all fiducial lists visible or invisible.

	Name: text to be displayed at this fiducial location
	Selected: flag set to checked if this fiducial is selected
	Visible : flag set to checked if this fiducial is visible
	Locked : flag set to checked if this fiducial is locked
	X : X axis location of this fiducial, corresponding to R in RAS
	Y : Y axis location of this fiducial, corresponding to A in RAS
	Z : Z axis location of this fiducial, corresponding to S in RAS

	Distance: distance between first two selected fiducials, updated as selection changes, fiducials are moved.

Click on a value and hit the 'Enter' key (or double click) on one of the X, Y, or Z position values to edit it manually. You can do the same on the fiducial name to change it. The default name is generated from the name of the list, which can be changed in the Data Module.

The distance between the first two selected fiducials in the list will be computed automatically and appear in a label below the list of fiducials. This distance is in milimetres.

To align slices with fiducials, move the fiducial while holding down the Control key. You can use the '`' (backtick) key to jump to the next fiducial, Control-` to jump backwards through the list.

Use the backspace or delete key to delete a fiducial over which you are hovering in 2D.

Argument Lists: Fiducials can be passed as a list of points to a command line module, for example to do ACPC registration. Only the points that are selected in the list are passed to the command line module, so you can adjust which points are used for calculating the output.

• Adjust Display Properties panel:

	Glyph Type: Select the glyph used to represent this point in 3D. There is a long list of glyph types available, each list can have a different glyph type, as well as colour and size properties. The default is the 2D starburst, but 3D glyphs are also available.
	Glyph Scale: Select the scale of the glyph. For the 3d glyphs (Sphere and Diamond3D), 1 corresponds to 1mm in diameter.
	Text Scale: Select the scale of the fiducial label text.
	Opacity: Select the opacity of the fiducial glyph and text. 0 = invisible.
	Visibility: Toggle the visibility of all fiducials in the list.
	Color: Select the color used to represent the fiducials when they are not selected.
	Selected Color: Select the color used to represent the fiducials when they are selected.

The following image shows what these types of glyphs look like in 3D:

Development

Dependencies

No other modules or packages are required for this module's use.

Known bugs

Follow this link to the Slicer3 bug tracker.

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Source Code:

• vtkSlicerFiducialsGUI.cxx, vtkSlicerFiducialsGUI.h
• vtkSlicerFiducialListWidget.cxx, vtkSlicerFiducialListWidget.h
• vtkSlicerFiducialsLogic.cxx, vtkSlicerFiducialsLogic.h

Links to documentation generated by doxygen:

• vtkSlicerFiducialsGUI
• vtkSlicerFiducialListWidget
• vtkSlicerFiducialsLogic

More Information

Acknowledgment

This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.