Projects:ARRA:miAnnotation

2010-06-15T00:23:04Z

[http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM Return to miAnnotation]

__NOTOC__
===miAnnotation===
miAnnotation (Medical Image Annotation)

{|
|[[Image:miAnnotation-GUI.jpg|thumb|560px|GUI]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Kilian Pohl: pohl@csail.mit.edu
* Yong Zhang: yzhang@bwh.harvard.edu

===Module Description===
The miAnnotation Module is designed for users to annotate medical images to capture information latent in the scans.

== Usage ==
Eight (8) different types of annotations can be created in the following ways:

*Region Of Interest (ROI): Click on the ROI Icon [[File:miAnnotation-ROI.jpg]] on the middle panel of the miAnnotation main panel, a new ROI annotation will then be created on the right-hand-side 3D view. There are seven (7) control points on the ROI annotation for the user to interact with. The six (6) control points located on the six surface of the ROI box can be dragged using mouse left-button to enlarge or shrink the box. The one (1) control point located in the center of the box can be dragged using mouse left-button to relocate the box in the 3D view. A new ROI entry will also be created in the annotation table. The properties of the ROI annotation can be edited by clicking the edit icon [[File:miAnnotation-EditROI.jpg]] in the annotation table.

*Text: Click on the text Icon [[File:miAnnotation-text.jpg]] on the middle panel of the miAnnotation main panel, a new text annotation will then be created on the right-hand-side 3D view. The default location of the new text annotation is on the bottom left corner of the viewer. The user can move the text annotation to any other locations by clicking and dragging the text annotation using the mouse middle-button. A new text entry will also be created in the annotation table. The content of the text annotation can be edited from the entry in the annotation table. The properties of the text annotation can be edited by clicking the edit icon [[File:miAnnotation-EditText.jpg]] in the annotation table.

*Ruler: Click on the ruler Icon [[File:miAnnotation-ruler.jpg]] on the middle panel of the miAnnotation main panel, a new ruler annotation will then be created on the right-hand-side 3D view. The default location of the new ruler annotation is in the middle of the viewer spanned from left to right. The user can click and drag any one of the two control points of the ruler annotation to interact with it. A new ruler entry will also be created in the annotation table. The value of the ruler measurement can be automatically updated when the user interact with the ruler. The properties of the ruler annotation can be edited by clicking the edit icon [[File:miAnnotation-EditRuler.jpg]] in the annotation table.

*Angle: Click on the angle Icon [[File:miAnnotation-angle.jpg]] on the middle panel of the miAnnotation main panel, a new angle annotation will then be initialized on the right-hand-side 3D view. The users are required to manually click three (3) times in the 3D viewer using mouse left-button to create the real angle annotation. After creating the angle annotation, the user can click and drag any one of the three control points of the angle annotation to interact with it. A new angle entry will also be created in the annotation table. The value of the angle measurement can be automatically updated when the user interact with the angle. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditAngle.jpg]] in the annotation table.

*Fiducial: Click on the fiducial Icon [[File:miAnnotation-point.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in any of the 2D viewers using mouse left-button to create a new fiducial annotation. The new annotation will also be displayed in the 3D viewer. After creating the annotation, the user can click and drag it to interact with it. A new fiducial entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPoint.jpg]] in the annotation table.

*Bidimensional Lines: Click on the bidimensional lines Icon [[File:miAnnotation-Polyline.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in the 3D viewers using mouse left-button to create two lines. These two lines are automatically orthogonal. After creating the annotation, the user can click and drag any of the four control points to interact with it. A new bidimensional line entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPolyline.jpg]] in the annotation table.

*Spline: Click on the spline Icon [[File:miAnnotation-Spline.jpg]] on the middle panel of the miAnnotation main panel, then a new spline annotation point is created right in the center of the 3d viewer. The users are able to manually click and drag the spline point using mouse left-button to other locations in the 3D viewer. Up to five (5) points can be clicked and dragged from the initial location of the spline annotation. After creating the annotation, the user can click and drag any of the five control points to form different splines to fit their needs. Or the user can click and drag the entire spline annotation to move it as a whole. A new spline entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditSpline.jpg]] in the annotation table.

*Sticky Note: Click on the stick note Icon [[File:miAnnotation-Note.jpg]] on the middle panel of the miAnnotation main panel, then a new stick note is created. There are no displays of the note in any of the 2D or 3D viewers. After creating the annotation, a new sticky note entry will be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditNote.jpg]] in the annotation table.

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1: This module is useful for basic measurements of volume, area, length, angle.
* Use Case 2: Use eight different annotations to annotate medical images.

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial (coming soon)
* Data Set (coming soon)

===Quick Tour of Features and Use===
* '''miAnnotation Main Panel''':
{|
|
* '''Upper Panel:'''
**8 different annotation types
**controls for mouse modes

* '''Middle Panel:'''
**A table contains all annotations
**Edit annotation properties
**Edit annotation table

* '''Lower Panel:'''
**Save as text format
**Save screen shot
**Save entire MRML structure
**Save report as HTML format

|[[Image:miAnnotation-MainPanel.jpg|thumb|560px|Main Panel]]
|}

* '''Edit annotation table''':
** Click hide/unhide icon [[File:miAnnotation-Visibility.jpg]] to hide and unhide a single annotation in the viewers
** Click lock/unlock icon [[File:miAnnotation-Lock.jpg]] to lock and unlock a single annotation in the viewers to enable and disable the user interaction

* '''Save Annotations''':
{|
|
*Save screen shot
*Save entire MRML structure
*Save HTML
|[[Image:miAnnotation-Screenshot.jpg|thumb|560px|Save Screen Shot]]
[[Image:miAnnotation-MRML.jpg|thumb|560px|Save MRML Structure]]
[[Image:miAnnotation-HTML.jpg|thumb|560px|Save HTML Format]]
|}

===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)===

From Slicer3.5 to Slicer3.6, the underlying implementation of the fiducials in the 3D scene has been changed to use vtkSeedWidgets.

===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/GUI/vtkSlicerSeedWidgetClass.cxx vtkSlicerSeedWidgetClass.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/vtkSlicerSeedWidgetClass.h vtkSlicerSeedWidgetClass.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===

Annotation Documentation

2010-06-09T00:48:26Z

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

[http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM Return to miAnnotation]

__NOTOC__
===miAnnotation===
miAnnotation (Medical Image Annotation)

{|
|[[Image:miAnnotation-GUI.jpg|thumb|560px|GUI]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Kilian Pohl: pohl@csail.mit.edu
* Yong Zhang: yzhang@bwh.harvard.edu

===Module Description===
The miAnnotation Module is designed for users to annotate medical images to capture information latent in the scans.

== Usage ==
Eight (8) different types of annotations can be created in the following ways:

*Region Of Interest (ROI): Click on the ROI Icon [[File:miAnnotation-ROI.jpg]] on the middle panel of the miAnnotation main panel, a new ROI annotation will then be created on the right-hand-side 3D view. There are seven (7) control points on the ROI annotation for the user to interact with. The six (6) control points located on the six surface of the ROI box can be dragged using mouse left-button to enlarge or shrink the box. The one (1) control point located in the center of the box can be dragged using mouse left-button to relocate the box in the 3D view. A new ROI entry will also be created in the annotation table. The properties of the ROI annotation can be edited by clicking the edit icon [[File:miAnnotation-EditROI.jpg]] in the annotation table.

*Text: Click on the text Icon [[File:miAnnotation-text.jpg]] on the middle panel of the miAnnotation main panel, a new text annotation will then be created on the right-hand-side 3D view. The default location of the new text annotation is on the bottom left corner of the viewer. The user can move the text annotation to any other locations by clicking and dragging the text annotation using the mouse middle-button. A new text entry will also be created in the annotation table. The content of the text annotation can be edited from the entry in the annotation table. The properties of the text annotation can be edited by clicking the edit icon [[File:miAnnotation-EditText.jpg]] in the annotation table.

*Ruler: Click on the ruler Icon [[File:miAnnotation-ruler.jpg]] on the middle panel of the miAnnotation main panel, a new ruler annotation will then be created on the right-hand-side 3D view. The default location of the new ruler annotation is in the middle of the viewer spanned from left to right. The user can click and drag any one of the two control points of the ruler annotation to interact with it. A new ruler entry will also be created in the annotation table. The value of the ruler measurement can be automatically updated when the user interact with the ruler. The properties of the ruler annotation can be edited by clicking the edit icon [[File:miAnnotation-EditRuler.jpg]] in the annotation table.

*Angle: Click on the angle Icon [[File:miAnnotation-angle.jpg]] on the middle panel of the miAnnotation main panel, a new angle annotation will then be initialized on the right-hand-side 3D view. The users are required to manually click three (3) times in the 3D viewer using mouse left-button to create the real angle annotation. After creating the angle annotation, the user can click and drag any one of the three control points of the angle annotation to interact with it. A new angle entry will also be created in the annotation table. The value of the angle measurement can be automatically updated when the user interact with the angle. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditAngle.jpg]] in the annotation table.

*Fiducial: Click on the fiducial Icon [[File:miAnnotation-point.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in any of the 2D viewers using mouse left-button to create a new fiducial annotation. The new annotation will also be displayed in the 3D viewer. After creating the annotation, the user can click and drag it to interact with it. A new fiducial entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPoint.jpg]] in the annotation table.

*Bidimensional Lines: Click on the bidimensional lines Icon [[File:miAnnotation-Polyline.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in the 3D viewers using mouse left-button to create two lines. These two lines are automatically orthogonal. After creating the annotation, the user can click and drag any of the four control points to interact with it. A new bidimensional line entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPolyline.jpg]] in the annotation table.

*Spline: Click on the spline Icon [[File:miAnnotation-Spline.jpg]] on the middle panel of the miAnnotation main panel, then a new spline annotation point is created right in the center of the 3d viewer. The users are able to manually click and drag the spline point using mouse left-button to other locations in the 3D viewer. Up to five (5) points can be clicked and dragged from the initial location of the spline annotation. After creating the annotation, the user can click and drag any of the five control points to form different splines to fit their needs. Or the user can click and drag the entire spline annotation to move it as a whole. A new spline entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditSpline.jpg]] in the annotation table.

*Sticky Note: Click on the stick note Icon [[File:miAnnotation-Note.jpg]] on the middle panel of the miAnnotation main panel, then a new stick note is created. There are no displays of the note in any of the 2D or 3D viewers. After creating the annotation, a new sticky note entry will be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditNote.jpg]] in the annotation table.

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1: This module is useful for basic measurements of volume, area, length, angle.
* Use Case 2: Use eight different annotations to annotate medical images.

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial (coming soon)
* Data Set (coming soon)

===Quick Tour of Features and Use===
* '''miAnnotation Main Panel''':
{|
|
* '''Upper Panel:'''
**8 different annotation types
**controls for mouse modes

* '''Middle Panel:'''
**A table contains all annotations
**Edit annotation properties
**Edit annotation table

* '''Lower Panel:'''
**Save as text format
**Save screen shot
**Save entire MRML structure
**Save report as HTML format

|[[Image:miAnnotation-MainPanel.jpg|thumb|560px|Main Panel]]
|}

* '''Edit annotation table''':
** Click hide/unhide icon [[File:miAnnotation-Visibility.jpg]] to hide and unhide a single annotation in the viewers
** Click lock/unlock icon [[File:miAnnotation-Lock.jpg]] to lock and unlock a single annotation in the viewers to enable and disable the user interaction

* '''Save Annotations''':
**Save screen shot
[[Image:miAnnotation-Screenshot.jpg|thumb|560px|Save Screen Shot]]
**Save entire MRML structure
[[Image:miAnnotation-MRML.jpg|thumb|560px|Save MRML Structure]]
**Save HTML
[[Image:miAnnotation-HTML.jpg|thumb|560px|Save HTML Format]]

===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)===

From Slicer3.5 to Slicer3.6, the underlying implementation of the fiducials in the 3D scene has been changed to use vtkSeedWidgets.

===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/GUI/vtkSlicerSeedWidgetClass.cxx vtkSlicerSeedWidgetClass.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/vtkSlicerSeedWidgetClass.h vtkSlicerSeedWidgetClass.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===

File:MiAnnotation-Lock.jpg

2010-06-09T00:45:05Z

Yzhang:

File:MiAnnotation-Visibility.jpg

2010-06-09T00:44:51Z

Yzhang:

Annotation Documentation

2010-06-09T00:44:36Z

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

[http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM Return to miAnnotation]

__NOTOC__
===miAnnotation===
miAnnotation (Medical Image Annotation)

{|
|[[Image:miAnnotation-GUI.jpg|thumb|560px|GUI]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Kilian Pohl: pohl@csail.mit.edu
* Yong Zhang: yzhang@bwh.harvard.edu

===Module Description===
The miAnnotation Module is designed for users to annotate medical images to capture information latent in the scans.

== Usage ==
Eight (8) different types of annotations can be created in the following ways:

*Region Of Interest (ROI): Click on the ROI Icon [[File:miAnnotation-ROI.jpg]] on the middle panel of the miAnnotation main panel, a new ROI annotation will then be created on the right-hand-side 3D view. There are seven (7) control points on the ROI annotation for the user to interact with. The six (6) control points located on the six surface of the ROI box can be dragged using mouse left-button to enlarge or shrink the box. The one (1) control point located in the center of the box can be dragged using mouse left-button to relocate the box in the 3D view. A new ROI entry will also be created in the annotation table. The properties of the ROI annotation can be edited by clicking the edit icon [[File:miAnnotation-EditROI.jpg]] in the annotation table.

*Text: Click on the text Icon [[File:miAnnotation-text.jpg]] on the middle panel of the miAnnotation main panel, a new text annotation will then be created on the right-hand-side 3D view. The default location of the new text annotation is on the bottom left corner of the viewer. The user can move the text annotation to any other locations by clicking and dragging the text annotation using the mouse middle-button. A new text entry will also be created in the annotation table. The content of the text annotation can be edited from the entry in the annotation table. The properties of the text annotation can be edited by clicking the edit icon [[File:miAnnotation-EditText.jpg]] in the annotation table.

*Ruler: Click on the ruler Icon [[File:miAnnotation-ruler.jpg]] on the middle panel of the miAnnotation main panel, a new ruler annotation will then be created on the right-hand-side 3D view. The default location of the new ruler annotation is in the middle of the viewer spanned from left to right. The user can click and drag any one of the two control points of the ruler annotation to interact with it. A new ruler entry will also be created in the annotation table. The value of the ruler measurement can be automatically updated when the user interact with the ruler. The properties of the ruler annotation can be edited by clicking the edit icon [[File:miAnnotation-EditRuler.jpg]] in the annotation table.

*Angle: Click on the angle Icon [[File:miAnnotation-angle.jpg]] on the middle panel of the miAnnotation main panel, a new angle annotation will then be initialized on the right-hand-side 3D view. The users are required to manually click three (3) times in the 3D viewer using mouse left-button to create the real angle annotation. After creating the angle annotation, the user can click and drag any one of the three control points of the angle annotation to interact with it. A new angle entry will also be created in the annotation table. The value of the angle measurement can be automatically updated when the user interact with the angle. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditAngle.jpg]] in the annotation table.

*Fiducial: Click on the fiducial Icon [[File:miAnnotation-point.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in any of the 2D viewers using mouse left-button to create a new fiducial annotation. The new annotation will also be displayed in the 3D viewer. After creating the annotation, the user can click and drag it to interact with it. A new fiducial entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPoint.jpg]] in the annotation table.

*Bidimensional Lines: Click on the bidimensional lines Icon [[File:miAnnotation-Polyline.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in the 3D viewers using mouse left-button to create two lines. These two lines are automatically orthogonal. After creating the annotation, the user can click and drag any of the four control points to interact with it. A new bidimensional line entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPolyline.jpg]] in the annotation table.

*Spline: Click on the spline Icon [[File:miAnnotation-Spline.jpg]] on the middle panel of the miAnnotation main panel, then a new spline annotation point is created right in the center of the 3d viewer. The users are able to manually click and drag the spline point using mouse left-button to other locations in the 3D viewer. Up to five (5) points can be clicked and dragged from the initial location of the spline annotation. After creating the annotation, the user can click and drag any of the five control points to form different splines to fit their needs. Or the user can click and drag the entire spline annotation to move it as a whole. A new spline entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditSpline.jpg]] in the annotation table.

*Sticky Note: Click on the stick note Icon [[File:miAnnotation-Note.jpg]] on the middle panel of the miAnnotation main panel, then a new stick note is created. There are no displays of the note in any of the 2D or 3D viewers. After creating the annotation, a new sticky note entry will be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditNote.jpg]] in the annotation table.

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1: This module is useful for basic measurements of volume, area, length, angle.
* Use Case 2: Use eight different annotations to annotate medical images.

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial (coming soon)
* Data Set (coming soon)

===Quick Tour of Features and Use===
* '''miAnnotation Main Panel''':
{|
|
* '''Upper Panel:'''
**8 different annotation types
**controls for mouse modes

* '''Middle Panel:'''
**A table contains all annotations
**Edit annotation properties
**Edit annotation table

* '''Lower Panel:'''
**Save as text format
**Save screen shot
**Save entire MRML structure
**Save report as HTML format

|[[Image:miAnnotation-MainPanel.jpg|thumb|560px|Main Panel]]
|}

* '''Edit annotation table''':
** Click hide/unhide icon [[File:miAnnotation-Visibility.jpg]] to hide and unhide a single annotation in the viewers
** Click lock/unlock icon [[File:miAnnotation-Lock.jpg]] to lock and unlock a single annotation in the viewers to enable and disable the user interaction

===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)===

From Slicer3.5 to Slicer3.6, the underlying implementation of the fiducials in the 3D scene has been changed to use vtkSeedWidgets.

===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/GUI/vtkSlicerSeedWidgetClass.cxx vtkSlicerSeedWidgetClass.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/vtkSlicerSeedWidgetClass.h vtkSlicerSeedWidgetClass.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===

Annotation Documentation

2010-06-09T00:40:50Z

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

[http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM Return to miAnnotation]

__NOTOC__
===miAnnotation===
miAnnotation (Medical Image Annotation)

{|
|[[Image:miAnnotation-GUI.jpg|thumb|560px|GUI]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Kilian Pohl: pohl@csail.mit.edu
* Yong Zhang: yzhang@bwh.harvard.edu

===Module Description===
The miAnnotation Module is designed for users to annotate medical images to capture information latent in the scans.

== Usage ==
Eight (8) different types of annotations can be created in the following ways:

*Region Of Interest (ROI): Click on the ROI Icon [[File:miAnnotation-ROI.jpg]] on the middle panel of the miAnnotation main panel, a new ROI annotation will then be created on the right-hand-side 3D view. There are seven (7) control points on the ROI annotation for the user to interact with. The six (6) control points located on the six surface of the ROI box can be dragged using mouse left-button to enlarge or shrink the box. The one (1) control point located in the center of the box can be dragged using mouse left-button to relocate the box in the 3D view. A new ROI entry will also be created in the annotation table. The properties of the ROI annotation can be edited by clicking the edit icon [[File:miAnnotation-EditROI.jpg]] in the annotation table.

*Text: Click on the text Icon [[File:miAnnotation-text.jpg]] on the middle panel of the miAnnotation main panel, a new text annotation will then be created on the right-hand-side 3D view. The default location of the new text annotation is on the bottom left corner of the viewer. The user can move the text annotation to any other locations by clicking and dragging the text annotation using the mouse middle-button. A new text entry will also be created in the annotation table. The content of the text annotation can be edited from the entry in the annotation table. The properties of the text annotation can be edited by clicking the edit icon [[File:miAnnotation-EditText.jpg]] in the annotation table.

*Ruler: Click on the ruler Icon [[File:miAnnotation-ruler.jpg]] on the middle panel of the miAnnotation main panel, a new ruler annotation will then be created on the right-hand-side 3D view. The default location of the new ruler annotation is in the middle of the viewer spanned from left to right. The user can click and drag any one of the two control points of the ruler annotation to interact with it. A new ruler entry will also be created in the annotation table. The value of the ruler measurement can be automatically updated when the user interact with the ruler. The properties of the ruler annotation can be edited by clicking the edit icon [[File:miAnnotation-EditRuler.jpg]] in the annotation table.

*Angle: Click on the angle Icon [[File:miAnnotation-angle.jpg]] on the middle panel of the miAnnotation main panel, a new angle annotation will then be initialized on the right-hand-side 3D view. The users are required to manually click three (3) times in the 3D viewer using mouse left-button to create the real angle annotation. After creating the angle annotation, the user can click and drag any one of the three control points of the angle annotation to interact with it. A new angle entry will also be created in the annotation table. The value of the angle measurement can be automatically updated when the user interact with the angle. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditAngle.jpg]] in the annotation table.

*Fiducial: Click on the fiducial Icon [[File:miAnnotation-point.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in any of the 2D viewers using mouse left-button to create a new fiducial annotation. The new annotation will also be displayed in the 3D viewer. After creating the annotation, the user can click and drag it to interact with it. A new fiducial entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPoint.jpg]] in the annotation table.

*Bidimensional Lines: Click on the bidimensional lines Icon [[File:miAnnotation-Polyline.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in the 3D viewers using mouse left-button to create two lines. These two lines are automatically orthogonal. After creating the annotation, the user can click and drag any of the four control points to interact with it. A new bidimensional line entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPolyline.jpg]] in the annotation table.

*Spline: Click on the spline Icon [[File:miAnnotation-Spline.jpg]] on the middle panel of the miAnnotation main panel, then a new spline annotation point is created right in the center of the 3d viewer. The users are able to manually click and drag the spline point using mouse left-button to other locations in the 3D viewer. Up to five (5) points can be clicked and dragged from the initial location of the spline annotation. After creating the annotation, the user can click and drag any of the five control points to form different splines to fit their needs. Or the user can click and drag the entire spline annotation to move it as a whole. A new spline entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditSpline.jpg]] in the annotation table.

*Sticky Note: Click on the stick note Icon [[File:miAnnotation-Note.jpg]] on the middle panel of the miAnnotation main panel, then a new stick note is created. There are no displays of the note in any of the 2D or 3D viewers. After creating the annotation, a new sticky note entry will be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditNote.jpg]] in the annotation table.

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1: This module is useful for basic measurements of volume, area, length, angle.
* Use Case 2: Use eight different annotations to annotate medical images.

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial (coming soon)
* Data Set (coming soon)

===Quick Tour of Features and Use===
* '''miAnnotation Main Panel''':
{|
|
* '''Upper Panel:'''
**8 different annotation types
**controls for mouse modes

* '''Middle Panel:'''
**A table contains all annotations
**Edit annotation properties
**Edit annotation table

* '''Lower Panel:'''
**Save as text format
**Save screen shot
**Save entire MRML structure
**Save report as HTML format

|[[Image:miAnnotation-MainPanel.jpg|thumb|560px|Main Panel]]
|}

* '''miAnnotation Main Panel''':

===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)===

From Slicer3.5 to Slicer3.6, the underlying implementation of the fiducials in the 3D scene has been changed to use vtkSeedWidgets.

===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/GUI/vtkSlicerSeedWidgetClass.cxx vtkSlicerSeedWidgetClass.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/vtkSlicerSeedWidgetClass.h vtkSlicerSeedWidgetClass.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===

Annotation Documentation

2010-06-09T00:39:39Z

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

[http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM Return to miAnnotation]

__NOTOC__
===miAnnotation===
miAnnotation (Medical Image Annotation)

{|
|[[Image:miAnnotation-GUI.jpg|thumb|560px|GUI]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Kilian Pohl: pohl@csail.mit.edu
* Yong Zhang: yzhang@bwh.harvard.edu

===Module Description===
The miAnnotation Module is designed for users to annotate medical images to capture information latent in the scans.

== Usage ==
Eight (8) different types of annotations can be created in the following ways:

*Region Of Interest (ROI): Click on the ROI Icon [[File:miAnnotation-ROI.jpg]] on the middle panel of the miAnnotation main panel, a new ROI annotation will then be created on the right-hand-side 3D view. There are seven (7) control points on the ROI annotation for the user to interact with. The six (6) control points located on the six surface of the ROI box can be dragged using mouse left-button to enlarge or shrink the box. The one (1) control point located in the center of the box can be dragged using mouse left-button to relocate the box in the 3D view. A new ROI entry will also be created in the annotation table. The properties of the ROI annotation can be edited by clicking the edit icon [[File:miAnnotation-EditROI.jpg]] in the annotation table.

*Text: Click on the text Icon [[File:miAnnotation-text.jpg]] on the middle panel of the miAnnotation main panel, a new text annotation will then be created on the right-hand-side 3D view. The default location of the new text annotation is on the bottom left corner of the viewer. The user can move the text annotation to any other locations by clicking and dragging the text annotation using the mouse middle-button. A new text entry will also be created in the annotation table. The content of the text annotation can be edited from the entry in the annotation table. The properties of the text annotation can be edited by clicking the edit icon [[File:miAnnotation-EditText.jpg]] in the annotation table.

*Ruler: Click on the ruler Icon [[File:miAnnotation-ruler.jpg]] on the middle panel of the miAnnotation main panel, a new ruler annotation will then be created on the right-hand-side 3D view. The default location of the new ruler annotation is in the middle of the viewer spanned from left to right. The user can click and drag any one of the two control points of the ruler annotation to interact with it. A new ruler entry will also be created in the annotation table. The value of the ruler measurement can be automatically updated when the user interact with the ruler. The properties of the ruler annotation can be edited by clicking the edit icon [[File:miAnnotation-EditRuler.jpg]] in the annotation table.

*Angle: Click on the angle Icon [[File:miAnnotation-angle.jpg]] on the middle panel of the miAnnotation main panel, a new angle annotation will then be initialized on the right-hand-side 3D view. The users are required to manually click three (3) times in the 3D viewer using mouse left-button to create the real angle annotation. After creating the angle annotation, the user can click and drag any one of the three control points of the angle annotation to interact with it. A new angle entry will also be created in the annotation table. The value of the angle measurement can be automatically updated when the user interact with the angle. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditAngle.jpg]] in the annotation table.

*Fiducial: Click on the fiducial Icon [[File:miAnnotation-point.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in any of the 2D viewers using mouse left-button to create a new fiducial annotation. The new annotation will also be displayed in the 3D viewer. After creating the annotation, the user can click and drag it to interact with it. A new fiducial entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPoint.jpg]] in the annotation table.

*Bidimensional Lines: Click on the bidimensional lines Icon [[File:miAnnotation-Polyline.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in the 3D viewers using mouse left-button to create two lines. These two lines are automatically orthogonal. After creating the annotation, the user can click and drag any of the four control points to interact with it. A new bidimensional line entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPolyline.jpg]] in the annotation table.

*Spline: Click on the spline Icon [[File:miAnnotation-Spline.jpg]] on the middle panel of the miAnnotation main panel, then a new spline annotation point is created right in the center of the 3d viewer. The users are able to manually click and drag the spline point using mouse left-button to other locations in the 3D viewer. Up to five (5) points can be clicked and dragged from the initial location of the spline annotation. After creating the annotation, the user can click and drag any of the five control points to form different splines to fit their needs. Or the user can click and drag the entire spline annotation to move it as a whole. A new spline entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditSpline.jpg]] in the annotation table.

*Sticky Note: Click on the stick note Icon [[File:miAnnotation-Note.jpg]] on the middle panel of the miAnnotation main panel, then a new stick note is created. There are no displays of the note in any of the 2D or 3D viewers. After creating the annotation, a new sticky note entry will be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditNote.jpg]] in the annotation table.

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1: This module is useful for basic measurements of volume, area, length, angle.
* Use Case 2: Use eight different annotations to annotate medical images.

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial (coming soon)
* Data Set (coming soon)

===Quick Tour of Features and Use===
miAnnotation Main Panel:
{|
|
* '''Upper Panel:'''
**8 different annotation types
**controls for mouse modes

* '''Middle Panel:'''
**A table contains all annotations
**Edit annotation properties
**Edit annotation table

* '''Lower Panel:'''
**Save as text format
**Save screen shot
**Save entire MRML structure
**Save report as HTML format

|[[Image:miAnnotation-MainPanel.jpg|thumb|560px|Main Panel]]
|}

===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)===

From Slicer3.5 to Slicer3.6, the underlying implementation of the fiducials in the 3D scene has been changed to use vtkSeedWidgets.

===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/GUI/vtkSlicerSeedWidgetClass.cxx vtkSlicerSeedWidgetClass.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/vtkSlicerSeedWidgetClass.h vtkSlicerSeedWidgetClass.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===

Annotation Documentation

2010-06-09T00:39:25Z

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

[http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM Return to miAnnotation]

__NOTOC__
===miAnnotation===
miAnnotation (Medical Image Annotation)

{|
|[[Image:miAnnotation-GUI.jpg|thumb|560px|GUI]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Kilian Pohl: pohl@csail.mit.edu
* Yong Zhang: yzhang@bwh.harvard.edu

===Module Description===
The miAnnotation Module is designed for users to annotate medical images to capture information latent in the scans.

== Usage ==
Eight (8) different types of annotations can be created in the following ways:

*Region Of Interest (ROI): Click on the ROI Icon [[File:miAnnotation-ROI.jpg]] on the middle panel of the miAnnotation main panel, a new ROI annotation will then be created on the right-hand-side 3D view. There are seven (7) control points on the ROI annotation for the user to interact with. The six (6) control points located on the six surface of the ROI box can be dragged using mouse left-button to enlarge or shrink the box. The one (1) control point located in the center of the box can be dragged using mouse left-button to relocate the box in the 3D view. A new ROI entry will also be created in the annotation table. The properties of the ROI annotation can be edited by clicking the edit icon [[File:miAnnotation-EditROI.jpg]] in the annotation table.

*Text: Click on the text Icon [[File:miAnnotation-text.jpg]] on the middle panel of the miAnnotation main panel, a new text annotation will then be created on the right-hand-side 3D view. The default location of the new text annotation is on the bottom left corner of the viewer. The user can move the text annotation to any other locations by clicking and dragging the text annotation using the mouse middle-button. A new text entry will also be created in the annotation table. The content of the text annotation can be edited from the entry in the annotation table. The properties of the text annotation can be edited by clicking the edit icon [[File:miAnnotation-EditText.jpg]] in the annotation table.

*Ruler: Click on the ruler Icon [[File:miAnnotation-ruler.jpg]] on the middle panel of the miAnnotation main panel, a new ruler annotation will then be created on the right-hand-side 3D view. The default location of the new ruler annotation is in the middle of the viewer spanned from left to right. The user can click and drag any one of the two control points of the ruler annotation to interact with it. A new ruler entry will also be created in the annotation table. The value of the ruler measurement can be automatically updated when the user interact with the ruler. The properties of the ruler annotation can be edited by clicking the edit icon [[File:miAnnotation-EditRuler.jpg]] in the annotation table.

*Angle: Click on the angle Icon [[File:miAnnotation-angle.jpg]] on the middle panel of the miAnnotation main panel, a new angle annotation will then be initialized on the right-hand-side 3D view. The users are required to manually click three (3) times in the 3D viewer using mouse left-button to create the real angle annotation. After creating the angle annotation, the user can click and drag any one of the three control points of the angle annotation to interact with it. A new angle entry will also be created in the annotation table. The value of the angle measurement can be automatically updated when the user interact with the angle. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditAngle.jpg]] in the annotation table.

*Fiducial: Click on the fiducial Icon [[File:miAnnotation-point.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in any of the 2D viewers using mouse left-button to create a new fiducial annotation. The new annotation will also be displayed in the 3D viewer. After creating the annotation, the user can click and drag it to interact with it. A new fiducial entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPoint.jpg]] in the annotation table.

*Bidimensional Lines: Click on the bidimensional lines Icon [[File:miAnnotation-Polyline.jpg]] on the middle panel of the miAnnotation main panel, then the users are required to manually click in the 3D viewers using mouse left-button to create two lines. These two lines are automatically orthogonal. After creating the annotation, the user can click and drag any of the four control points to interact with it. A new bidimensional line entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditPolyline.jpg]] in the annotation table.

*Spline: Click on the spline Icon [[File:miAnnotation-Spline.jpg]] on the middle panel of the miAnnotation main panel, then a new spline annotation point is created right in the center of the 3d viewer. The users are able to manually click and drag the spline point using mouse left-button to other locations in the 3D viewer. Up to five (5) points can be clicked and dragged from the initial location of the spline annotation. After creating the annotation, the user can click and drag any of the five control points to form different splines to fit their needs. Or the user can click and drag the entire spline annotation to move it as a whole. A new spline entry will also be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditSpline.jpg]] in the annotation table.

*Sticky Note: Click on the stick note Icon [[File:miAnnotation-Note.jpg]] on the middle panel of the miAnnotation main panel, then a new stick note is created. There are no displays of the note in any of the 2D or 3D viewers. After creating the annotation, a new sticky note entry will be created in the annotation table. The properties of the annotation can be edited by clicking the edit icon [[File:miAnnotation-EditNote.jpg]] in the annotation table.

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1: This module is useful for basic measurements of volume, area, length, angle.
* Use Case 2: Use eight different annotations to annotate medical images.

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial (coming soon)
* Data Set (coming soon)

===Quick Tour of Features and Use===
miAnnotation Main Panel:
{|
|
* '''Upper Panel:'''
**8 different annotation types
**controls for mouse modes

* '''Middle Panel:'''
**A table contains all annotations
**Edit annotation properties
**Edit annotation table

* '''Lower Panel:'''
**Save as text format
**Save screen shot
**Save entire MRML structure
**Save report as HTML format

|[[Image:miAnnotation-MainPanel.jpg|thumb|560px|Main Panel]]
|}

===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)===

From Slicer3.5 to Slicer3.6, the underlying implementation of the fiducials in the 3D scene has been changed to use vtkSeedWidgets.

===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/GUI/vtkSlicerSeedWidgetClass.cxx vtkSlicerSeedWidgetClass.cxx], [http://viewvc.slicer.org/viewcvs.cgi/trunk/Base/GUI/vtkSlicerSeedWidgetClass.h vtkSlicerSeedWidgetClass.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===

2010-06-09T00:21:30Z

Yzhang:

File:MiAnnotation-Note.jpg

2010-06-09T00:20:47Z

Yzhang:

File:MiAnnotation-EditSpline.jpg

2010-06-09T00:19:48Z

Yzhang: