Annotation Documentation
miAnnotation
miAnnotation (Medical Image Annotation)
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 Interests (ROI): Click on the ROI Icon
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.
- You can also place fiducials while in 'tranform view' mode by positioning the mouse over a 2D slice plane in the Slice view windows (it must be the active window) and pressing the 'p' key.
- You can also add a new fiducial from the Fiducials module GUI, using the add button: File:SlicerFiducialsAddNew-3.4.jpg. This places a new fiducial at the origin, (0,0,0).
Interaction tips:
- You can right click on a fiducial in the Fiducials GUI and that will jump all the slices to that location.
- You can right click and drag a fiducial in the 2D slice windows using the mouse in 'transform view' mode. 3D interactions are possible by clicking and dragging the fiducial glyph in the 3D window.
Hot Key bindings for this module
Use Cases, Examples
This module is especially appropriate for these use cases:
- Use Case 1: This module is useful for setting up lists of points to pass to Registration modules.
- Use Case 2: Use fiducials to annotate scenes.
Examples of the module in use:
- Example 1: Set down fiducials along the midline of a brain and the ACPC line and pass them into the ACPC transform module to calculate a transform from the two lists of fiducials.
- Example 2: Put down a fiducial and use it with the Fiducial Seeding tractography module to generate fibre tracts that go through the point defined by the fiducial.
Tutorials
Links to tutorials explaining how to use this module:
- Tutorial 1
- Data Set 1
Quick Tour of Features and Use
Annotated GUI layout: (see below for a detailed description of each element, listed by panel.)
File:UIDesignSlicer3.4FiducialsGUIDraft5Anno.png
- Modify All Fiducial Lists & Their Fiducial Points panel:
| File:SlicerFiducialsModifyAllPanel-3.4.png | ||
| Global Control of Fiducial Lists icons. | ||
| File:SlicerFiducialListsSelectAll-3.4.png Select all fiducial points from all lists. | File:SlicerFiducialListsSelectNone-3.4.png Deselect all fiducial points from all lists. | File:SlicerFiducialListsDeleteAll-3.4.png Delete all fiducials lists and the fiducials they contain. |
| File:SlicerHideExposeAllFiducialLists-3.4.png Hide or expose all fiducial lists (preserve fiducial visibility settings). | File:SlicerLockOrUnlock.png Lock or unlock all fidicuial lists so that they cannot or can be moved in 3D. | File:SlicerVisibleOrInvisible.png Set visibility on all fiducials in all fiducial lists (preserve hide/expose settings). |
- Modify a Selected Fiducial List & Its Fiducials panel:
| File:SlicerFiducialListDisplayPanelCollapsed-3.4.png | ||||
| Control a Selected List icons | ||||
| File:SlicerHideFiducialList.png File:SlicerExposeFiducialList.png Hide or expose the selected fiducial list (preserves fiducial visibility settings) | File:SlicerFiducialListLock-3.4.png File:SlicerFiducialListUnlock-3.4.png Lock or unlock the selected fiducial list. | File:SlicerVisibleOrInvisible.png Set visibility on all fiducials in the selected list | File:SlicerDeleteFiducialList-3.4.png Delete all fiducial points in the selected list and then delete the list. | |
- Add and Modify Individual Fiducials panel:
You can reset the positions of the fiducials in the table that appears in the Add, Configure and Delete section of the Fiducials GUI.
| File:SlicerFiducialsAddModifyIndividualFiducials-3.4.jpg | ||||
| Add & Modify Individual Fiducials icons. | ||||
| File:SlicerFiducialsSelectAllInList-3.4.png Select all fiducial points from this fiducial list. | File:SlicerFiducialsSelectNoneInList-3.4.png Deselect all fiducial points from this fiducial list. | File:SlicerFiducialsAddNew-3.4.jpg Add a fiducial point to the current fiducial list, at (0,0,0). | File:SlicerFiducialsUp.png Move last clicked fiducial up one in the list. | File:SlicerFiducialsDown.png Move last clicked fiducial down one in the list. |
| File:SlicerFiducialsDeleteLastClicked-3.4.png Delete the last fiducial that was clicked on in the table. | File:SlicerFiducialsDeleteAll-3.4.png Delete all fiducial points from this fiducial list. | |||
| File:SlicerFiducialsListBox-3.4.jpg |
| Selected: flag set to checked if this fiducial is selected |
| Visible : icon set to an open eye if this fiducial is visible, close if invisible. |
| Name: text to be displayed at this fiducial location |
| X : X axis location of this fiducial, corresponding to R in RAS |
| Y : Y axis location of this fiducial, corresponding to A in RAS |
| Z : Z axis location of this fiducial, corresponding to S in RAS |
| Locked : icon set to a closed lock if this fiducial is locked |
| File:SlicerFiducialsDistance-3.6.jpg | |
| Distance: distance between first two selected fiducials, updated as selection changes and fiducials are moved. | |
| List Distance: distance between all selected fiducials in list, updated as selection changes and fiducials are moved. | |
| Renumber Fiducials: Renumber the fiducials in this list. Removes any numbers from the ends of the labels and then appends a number denoting the current place in the list, starting from entered value, 0 if none. Note: does not affect the auto name generation for the next added fiducial. | Rename Fiducials: Rename the fiducials in this list. Preserves any numbers at the end of the labels. Note: does not affect the auto name generation for the next added fiducial - change the list name from the node selector. |
| Numbering Scheme: Set the numbering scheme used to assign integers to the next added fiducial in the list. UseID uses the point ID, UseIndex uses the list index of the point, UsePrevious increments the number at the end of the previous point. |
Click on a value and hit the 'Enter' key (or double click) on one of the X, Y, or Z position values to edit it manually. You can do the same on the fiducial name to change it. The default name is generated from the name of the list, which can be changed in the Data Module.
The distance between the first two selected fiducials in the list will be computed automatically and appear in a label below the list of fiducials. This distance is in milimetres.
To align slices with fiducials, move the fiducial while holding down the Control key. You can use the '`' (backtick) key to jump to the next fiducial, Control-` to jump backwards through the list.
Use the backspace or delete key to delete a fiducial over which you are hovering in 2D.
Argument Lists: Fiducials can be passed as a list of points to a command line module, for example to do ACPC registration. Only the points that are selected in the list are passed to the command line module, so you can adjust which points are used for calculating the output.
- Other List Display Properties panel:
| File:SlicerFiducialListDisplayPanelExpanded-3.4.png |
| Glyph Type: Select the glyph used to represent this point in 3D. There is a long list of glyph types available, each list can have a different glyph type, as well as colour and size properties. The default is the 2D starburst, but 3D glyphs are also available. |
| Selected Color: Select the color used to represent the fiducials when they are selected. |
| Unselected Color: Select the color used to represent the fiducials when they are not selected. |
| Glyph Scale: Select the scale of the glyph. For the 3d glyphs (Sphere and Diamond3D), 1 corresponds to 1mm in diameter. |
| Text Scale: Select the scale of the fiducial label text. |
| Opacity: Select the opacity of the fiducial glyph and text. 0 = invisible. |
| Ambient: Set the ambient material property for the fiducial glyph. |
| Diffuse: Set the diffuse material property for the fiducial glyph. |
| Specular: Set the specular material property for the fiducial glyph. |
| Power: Set the power material property for the fiducial glyph. |
The following image shows what these types of glyphs look like in 3D: File:SlicerFiducialsGlyphs3D-3.4.jpg
and in 2D (the 3D glyphs default to a star burst in 2D): File:SlicerFiducialsGlyphs2D-3.4.jpg
Loading and Saving Lists
Fiducial lists can be written out to disk using the File menu, Save option. The files can be loaded into Slicer via the File menu, Add Data interface.
Fiducial list files are plain text, with the extension fcvs.
An example file:
# 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
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
| 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:
| 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. 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 |
| 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 label,x,y,z,sel,vis. 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 Dashboard, these tests verify that the module is working on various platforms:
- vtkMRMLFiducialListNodeTest1 Libs/MRML/Testing/vtkMRMLFiducialListNodeTest1.cxx
- vtkMRMLFiducialListStorageNodeTest1 Libs/MRML/Testing/vtkMRMLFiducialListStorageNodeTest1.cxx
- Slicer3FiducialsTest1 Base/GUI/Testing/TestFiducials.tcl
- Slicer3FiducialsTest2 Base/GUI/Testing/TestFiducialsAdd.tcl
- Slicer3FiducialsTestGlyphs Base/GUI/Testing/TestFiducialsGlyphs.tcl
- Slicer3FiducialsTestChangeGlyphs Base/GUI/Testing/TestFiducialsAddSymbolScale.tcl
Known bugs
Follow this link to the Slicer3 bug tracker.
Usability issues
Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.
Source code & documentation
Source Code:
- vtkSlicerFiducialsGUI.cxx, vtkSlicerFiducialsGUI.h
- vtkSlicerFiducialListWidget.cxx, vtkSlicerFiducialListWidget.h
- vtkSlicerSeedWidgetClass.cxx, vtkSlicerSeedWidgetClass.h
- vtkSlicerFiducialsLogic.cxx, vtkSlicerFiducialsLogic.h
Links to documentation generated by doxygen:
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.
