Modules:Fiducials-Documentation-3.6 - Revision history

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Nicole: /* Tutorials */

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Tutorials

Nicole: /* Quick Tour of Features and Use */

2010-04-29T23:12:21Z

Quick Tour of Features and Use

Nicole: /* Usage */

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Usage

Nicole: /* Usage */

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Usage

Nicole: /* Use Cases, Examples */

2010-04-29T22:44:30Z

Use Cases, Examples

Nicole: /* Notes from the Developer(s) */

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Notes from the Developer(s)

Nicole: /* Source code & documentation */

2010-03-26T22:28:25Z

Source code & documentation

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2010-03-26T22:26:43Z

Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Fiducials=== Fiducials {| |[[Image:SlicerF…'

New page

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Fiducials===
Fiducials

{|
|[[Image:SlicerFiducialPointsPanel-3.4.png|thumb|280px|List of Fiducial Points]]
|[[Image:SlicerFiducialsGlyphs-3.4.jpg|thumb|560px|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-3.4.jpg]]. 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.

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1: This module is useful for setting up lists of points to pass to Registration modules and to annotate scenes.
* Use Case 2:

Examples of the module in use:

* Example 1: This module is useful for setting up lists of points to pass to Registration modules and to annotate scenes.
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

===Quick Tour of Features and Use===

Annotated GUI layout: (see below for a detailed description of each element, listed by panel.)

[[Image:UIDesignSlicer3.4FiducialsGUIDraft5Anno.png]]

* '''Modify All Fiducial Lists & Their Fiducial Points panel:'''
{| border="1"
|-
| rowspan="5"| [[Image:SlicerFiducialsModifyAllPanel-3.4.png]]
|-
| colspan="3" | '''Global Control of Fiducial Lists''' icons.
|- valign="top"
| [[Image:SlicerFiducialListsSelectAll-3.4.png]] Select all fiducial points from all lists.
| [[Image:SlicerFiducialListsSelectNone-3.4.png]] Deselect all fiducial points from all lists.
| [[image:SlicerFiducialListsDeleteAll-3.4.png]] Delete all fiducials lists and the fiducials they contain.
|-
| [[Image:SlicerHideExposeAllFiducialLists-3.4.png]] Hide or expose all fiducial lists (preserve fiducial visibility settings).
| [[Image:SlicerLockOrUnlock.png]] Lock or unlock all fidicuial lists so that they cannot or can be moved in 3D.
| [[Image:SlicerVisibleOrInvisible.png]] Set visibility on all fiducials in all fiducial lists (preserve hide/expose settings).
|}
* '''Modify a Selected Fiducial List & Its Fiducials panel:'''
{| border="1"
|-
| rowspan="5" | [[Image:SlicerFiducialListDisplayPanelCollapsed-3.4.png]]
|-
| colspan="5" | '''Control a Selected List''' icons
|- valign="top"
| [[Image:SlicerHideFiducialList.png]] [[Image:SlicerExposeFiducialList.png]] Hide or expose the selected fiducial list (preserves fiducial visibility settings)
| [[Image:SlicerFiducialListLock-3.4.png]] [[Image:SlicerFiducialListUnlock-3.4.png]] Lock or unlock the selected fiducial list.
| [[Image:SlicerVisibleOrInvisible.png]] Set visibility on all fiducials in the selected list
| [[Image:SlicerDeleteFiducialList-3.4.png]] Delete all fiducial points in the selected list and then delete the list.
|}
* '''Add and Modify Individual 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.
{| border="1"
|-
| rowspan="5"| [[Image:SlicerFiducialsAddModifyIndividualFiducials-3.4.jpg]]
|-
| colspan="5" | '''Add & Modify Individual Fiducials''' icons.
|- valign="top"
| [[image:SlicerFiducialsSelectAllInList-3.4.png]] Select all fiducial points from this fiducial list.
| [[image:SlicerFiducialsSelectNoneInList-3.4.png]] Deselect all fiducial points from this fiducial list.
| [[Image:SlicerFiducialsAddNew-3.4.jpg]] Add a fiducial point to the current fiducial list, at (0,0,0).
| [[Image:SlicerFiducialsUp.png]] Move last clicked fiducial up one in the list.
| [[Image:SlicerFiducialsDown.png]] Move last clicked fiducial down one in the list.
|-
| [[image:SlicerFiducialsDeleteLastClicked-3.4.png]] Delete the last fiducial that was clicked on in the table.
| [[image:SlicerFiducialsDeleteAll-3.4.png]] Delete all fiducial points from this fiducial list.
|}
{| border="1"
|-
| rowspan="8"| [[Image:SlicerFiducialsListBox-3.4.jpg]]
|-
| '''Selected''': flag set to checked if this fiducial is selected
|-
| '''Visible''' : icon set to an open eye if this fiducial is visible, close if invisible.
|-
| '''Name''': text to be displayed at this fiducial location
|-
| '''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
|-
| '''Locked''' : icon set to a closed lock if this fiducial is locked
|}
{| border="1"
|-
| rowspan="2"| [[Image:SlicerFiducialsDistance-3.4.jpg]]
|-
| '''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.

* '''Other List Display Properties panel:'''

{| border="1"
|-
| rowspan="11"| [[Image:SlicerFiducialListDisplayPanelExpanded-3.4.png]]
|-
| '''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.

[[Image:FiducialsGlyphTypes.jpg]]
|-
| '''Selected Color''': Select the color used to represent the fiducials when they are selected.
|-
| '''Unselected Color''': Select the color used to represent the fiducials when they are not selected.
|-
| '''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.
|-
| '''Ambient''': Set the ambient material property for the fiducial glyph.
|-
| '''Diffuse''': Set the diffuse material property for the fiducial glyph.
|-
| '''Specular''': Set the specular material property for the fiducial glyph.
|-
| '''Power''': Set the power material property for the fiducial glyph.
|}

The following image shows what these types of glyphs look like in 3D:
[[image:SlicerFiducialsGlyphs3D-3.4.jpg]]

and in 2D (the 3D glyphs default to a star burst in 2D):
[[Image:SlicerFiducialsGlyphs2D-3.4.jpg]]

===Loading and Saving Lists===

Fiducial lists can be written out to disk using the File menu, Save option. The files can be loaded into Slicer via the File menu, Add Data interface.

Fiducial list files are plain text, with the extension ''fcvs''.

An example file:

<pre>
# Fiducial List file /home/username/L.fcsv
# name = L
# numPoints = 5
# symbolScale = 5.5
# symbolType = 11
# visibility = 1
# textScale = 12.5
# color = 0.4,1,1
# selectedColor = 0.807843,0.560784,1
# opacity = 1
# ambient = 0
# diffuse = 1
# specular = 0
# power = 1
# locked = 0
# columns = label,x,y,z,sel,vis
L-P,-58.0508,64.4069,0,1,1
L-P1,31.7797,-1.69492,0,1,1
L-P2,-2.11864,-49.1527,0,0,1
L-P3,-72.4576,-54.2374,0,1,0
L-P4,-63.1356,3.38984,0,1,1
</pre>

Lines are commented out by placing a hash mark (#) at the beginning of the line. There is an optional header section that lists display options. If no display options are included, the defaults are used when the list is read into Slicer. The header line formats follow the description of the point format.

The points are listed one per line in the following format:

pointName,X,Y,Z,selected,visibility

{|border="1"
|pointName
|a text string that is displayed at the location of the fiducial.
|-
|X,Y,Z
| 3 floating points that represent the 3D RAS location of the fiducial, in mm.
|-
|selected
|an integer value, either 0 or 1, denoting if the fiducial is selected or not.
|-
|visibility
|an integer value, either 0 or 1, denoting if the fiducial is visible or not.
|}

The header section of the fiducial list file consists of lines starting with a hash mark and a space (# ). A keyword = value pair follows the space. The keyword is parsed and compared against the list of known keywords:

{|border="1"
|+Fiducial List file header
|Fiducial List file
|Path to the fiducial list file when it was last saved from Slicer.
|-
| name
| A name for the list, new points will be named according to this string and the point number
|-
| numPoints
| The number of points in the list, skipped for now, as the list is built up by adding a point for each line in the points section of the file
|-
|symbolScale
|Floating point, used to scale the glyphs for all the fiducial points.
|-
|symbolType
|Integer selected from the range representing glyph types, default is 11 for a star burst. <pre>0 Vertex2D
1 Dash2D
2 Cross2D
3 ThickCross2D
4 Triangle2D
5 Square2D
6 Circle2D
7 Diamond2D
8 Arrow2D
9 ThickArrow2D
10 HookedArrow2D
11 StarBurst2D
12 Sphere3D
13 Diamond3D</pre>
|-
|visibility
|Integer, 0 means the list as a whole is invisible, 1 means that any visible fiducial points are visible.
|-
|textScale
|Floating point number that is used to scale the label text for all the fiducial points
|-
|color
|Three comma separated floating point numbers that give the red, green, blue values to be used for the glyph and text when the fiducial is not selected.
|-
|selectedColor
|Three comma separated floating point numbers that give the red, green, blue values to be used for the glyph and text when the fiducial is selected.
|-
|opacity
|Floating point number 0.0-1.0, material property on the glyph
|-
|ambient
|Floating point number 0.0-1.0, material property on the glyph
|-
|diffuse
|Floating point number 0.0-1.0, material property on the glyph
|-
|specular
|Floating point number 0.0-1.0, material property on the glyph
|-
|power
|Floating point number 0.0-1.0, material property on the glyph
|-
|locked
|Integer, 1 means the list as a whole is locked (points can't be moved in the 2d or 3d windows), 0 means the list as a whole is unlocked.
|-
|columns
|This entry gives you the flexibility to reorder your data for each point, the default is <pre>label,x,y,z,sel,vis</pre>. It's a comma separated list of keywords giving the format of the following lines for each point.
|}

==Importing Lists into a Spreadsheet==

To import a fiducial list into OpenOffice.org's Calc, version 3.1.1:

#In Slicer3, open the File, Save dialog and select the fiducial list to save.
#Set the file name, ending with .fcsv, and the directory in which to save it
#Open OpenOffice.org's Calc
#Click on ''File, Open''
#Expand the File type menu
#Select '''Text CSV''' as the file type
#Make sure '''All Files''' is selected for the directory listing filter
#Browse to the directory in which you saved your .fcsv file and select it, then click ''Open''
#The Text Import window will pop up
#In the Separator options, set it so that only comma is selected (the color and selectedColor comment lines will get separated into columns, but so will the column s comment to give headers for the rows of points)
#Click ''Open'' and the import will finish, with the fiducial points starting on row 18

To open a list in Excel 2007:

#In Slicer3, open the ''File, Save'' dialog and select the fiducial list to save.
#Set the file name, ending with .fcsv, and the directory in which to save it
#Click on the symbol in the top left to open the menu, select ''Open'' (if ''Import'' is an option, use it instead)
#Set the filter to '''All Files (*.*)'''
#Browse to the directory in which you saved your .fcsv file and select it, then click ''Open''
#Text Import Wizard will open
#In Original Data Type, select '''Delimited'''
#Click ''Next''
#In Delimiters, select '''Comma''' only
#Click ''Next''
#The Column data format should be fine as '''General'''
#Click ''Finish''

== Development ==

===Notes from the Developer(s)===

===Dependencies===

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

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* vtkMRMLFiducialListNodeTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/MRML/Testing/vtkMRMLFiducialListNodeTest1.cxx Libs/MRML/Testing/vtkMRMLFiducialListNodeTest1.cxx]
* vtkMRMLFiducialListStorageNodeTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Libs/MRML/Testing/vtkMRMLFiducialListStorageNodeTest1.cxx Libs/MRML/Testing/vtkMRMLFiducialListStorageNodeTest1.cxx]
* Slicer3FiducialsTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/Testing/TestFiducials.tcl Base/GUI/Testing/TestFiducials.tcl]
* Slicer3FiducialsTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/Testing/TestFiducialsAdd.tcl Base/GUI/Testing/TestFiducialsAdd.tcl]
* Slicer3FiducialsTestGlyphs [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/Testing/TestFiducialsGlyphs.tcl Base/GUI/Testing/TestFiducialsGlyphs.tcl]
* Slicer3FiducialsTestChangeGlyphs [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/Testing/TestFiducialsAddSymbolScale.tcl Base/GUI/Testing/TestFiducialsAddSymbolScale.tcl]

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source Code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/vtkSlicerFiducialsGUI.cxx vtkSlicerFiducialsGUI.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/vtkSlicerFiducialsGUI.h vtkSlicerFiducialsGUI.h]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/vtkSlicerFiducialListWidget.cxx vtkSlicerFiducialListWidget.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/vtkSlicerFiducialListWidget.h vtkSlicerFiducialListWidget.h]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/Logic/vtkSlicerFiducialsLogic.cxx vtkSlicerFiducialsLogic.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/Logic/vtkSlicerFiducialsLogic.h vtkSlicerFiducialsLogic.h]

Links to documentation generated by doxygen:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkSlicerFiducialsGUI.html vtkSlicerFiducialsGUI]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkSlicerFiducialListWidget.html vtkSlicerFiducialListWidget]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkSlicerFiducialsLogic.html 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.

===References===

@@ Line 59: / Line 59: @@
 Links to tutorials explaining how to use this module:
-* [http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials Tutorial]
+* [http://www.slicer.org/w/img_auth.php/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials Tutorial]
 ** [http://wiki.na-mic.org/Wiki/index.php/File:Fiducials_TutorialContestSummer2010.zip Fiducials tutorial data set]

← Older revision		Revision as of 22:51, 29 April 2010
Line 40:		Line 40:

	*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.		*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.
		+
		+	[[Modules:EventBindings-3.6#Fiducials \| Hot Key bindings for this module]]

	===Use Cases, Examples===		===Use Cases, Examples===

← Older revision		Revision as of 22:48, 29 April 2010
Line 34:		Line 34:

	*You can also add a new fiducial from the Fiducials module GUI, using the add button: [[Image:SlicerFiducialsAddNew-3.4.jpg]]. This places a new fiducial at the origin, (0,0,0).		*You can also add a new fiducial from the Fiducials module GUI, using the add button: [[Image:SlicerFiducialsAddNew-3.4.jpg]]. This places a new fiducial at the origin, (0,0,0).
		+
		+	Interaction tips:
		+
		+	*You can right click on a fiducial in the Fiducials GUI and that will jump all the slices to that location.

	*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.		*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.

← Older revision		Revision as of 00:03, 17 April 2010
Line 328:		Line 328:

	===Notes from the Developer(s)===		===Notes from the Developer(s)===
		+
		+	From Slicer3.5 to Slicer3.6, the underlying implementation of the fiducials in the 3D scene has been changed to use vtkSeedWidgets.

	===Dependencies===		===Dependencies===

@@ Line 132: / Line 132: @@
 {| border="1"
 |-
-| rowspan="2"| [[Image:SlicerFiducialsDistance-3.4.jpg]]
+| rowspan="5"| [[Image:SlicerFiducialsDistance-3.6.jpg]]
 |-
-| '''Distance''': distance between first two selected fiducials, updated as selection changes, fiducials are moved.
+| '''Distance''': distance between first two selected fiducials, updated as selection changes and fiducials are moved.
 |}

@@ Line 41: / Line 41: @@
 This module is especially appropriate for these use cases:
-* Use Case 1: This module is useful for setting up lists of points to pass to Registration modules and to annotate scenes.
+* Use Case 1: This module is useful for setting up lists of points to pass to Registration modules.
-* Use Case 2:
+* Use Case 2: Use fiducials to annotate scenes.
 Examples of the module in use:
-* Example 1: This module is useful for setting up lists of points to pass to Registration modules and to annotate scenes.
+* Example 1: Set down fiducials along the midline of a brain and the ACPC line and pass them into the ACPC transform module to calculate a transform from the two lists of fiducials.
-* Example 2
+* Example 2: Put down a fiducial and use it with the Fiducial Seeding tractography module to generate fibre tracts that go through the point defined by the fiducial.
 ===Tutorials===

@@ Line 359: / Line 359: @@
 *[http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/vtkSlicerFiducialsGUI.cxx vtkSlicerFiducialsGUI.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/vtkSlicerFiducialsGUI.h vtkSlicerFiducialsGUI.h]
 *[http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/vtkSlicerFiducialListWidget.cxx vtkSlicerFiducialListWidget.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/vtkSlicerFiducialListWidget.h vtkSlicerFiducialListWidget.h]
 *[http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/Logic/vtkSlicerFiducialsLogic.cxx vtkSlicerFiducialsLogic.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/Logic/vtkSlicerFiducialsLogic.h vtkSlicerFiducialsLogic.h]

Modules:Fiducials-Documentation-3.6 - Revision history

Grundlett: Text replacement - "http://wiki.slicer.org/slicerWiki/images/" to "http://www.slicer.org/w/img_auth.php/"

Nicole: /* Tutorials */

Nicole: /* Quick Tour of Features and Use */

Nicole: /* Usage */

Nicole: /* Usage */

Nicole: /* Use Cases, Examples */

Nicole: /* Notes from the Developer(s) */

Nicole: /* Source code & documentation */

Nicole: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Fiducials=== Fiducials {| |[[Image:SlicerF…'

Nicole: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features NOTOC ===Fiducials=== Fiducials {| |[[Image:SlicerF…'