Annotations

Annotations existed on the previous c++ program. This program knows how to read annotations written by the c++ and any results saved via this program will be usable both here as well as in the c++ program.

• Measure
• Oblique
• Arrows
• Text
• Bookmarks
• Save

Measure

The 4 choices are (see distance demo and oblique distance demo)

• Line only (arrow) - useful for drawing attention to a particular feature by drawing a long line from the edge of the image to the feature of interest.
• Line - SUV - click first on the tumor and then in a "clear" area of the screen where the SUV text will appear.
• Distance - clicking on both sides of the object to be measured result in a line with the measured distance written at the end.
• Angle - 3 points define the angle whose value in degrees will be displayed.

The initial click will define the starting point with a yellow dot. The second point will define the line or distance. A third point is needed for an angle. If you notice that you placed the yellow dot in the wrong position, the easiest method is to click on the opposite image and then back where you wanted the point to be. For example, if you want a distance on the CT image and the first point is in the wrong position, click anywhere on the PET image and then back on the CT, this time in the correct position.

Another method is to click on the second point and then use Clear Last button to erase the mistaken measurement. Clear Last works on image currently being used. For example there is one set of measurements for the CT image and another for the PET image. If you wanted to change to delete measurements on the PET image when you have been working on the CT image, you first need to click on it and then use Clear Last.

Clear All erases the entire list of measurements on all images. Below the keys is a box showing the total number of measurements currently defined. In our example there are 20 measurements.

Hide Annotations is useful for temporarily hiding all the annotations: measurements, arrows and text. This allows careful inspection of the underlying data.

Oblique

As indicated in the above Oblique button, there is the possiblity to define oblique slices which can be useful to see the foot without overlapping bones. If there are previous measurements, use Clear All to delete them. Then in the sagittal view, use Line only (Arrow) or Distance to define the position and angle of interest.

Oblique (Help) will change to Oblique and you can press on it to see:

You can scroll through the slices using the mouse wheel. As is shown, you may use the magnifying glass to zoom and pan.

Arrows

This allows one of 4 predefined arrows to be placed on an image, where the size of the arrow is specified. In the example the up arrow has been chosen with size 12. The Clear Last and Clear All work the same as in Measure, in this case clearing the arrows. The box shows that 9 arrows are currently defined.

Thin Arrows allows on the fly changing of the arrow shape to show thinner arrows that cover up less data.

Text

When the program is first used there is only the option of typing text into the box manually and then clicking on the screen to position it. You may add a text file, generated by any text editor, to put in your own predefined text strings. It is strongly advised that the first line be empty and contain only a carriage return. This results in a blank string as the default. After that put in your predefined strings separated by carriage returns. Finally save the file with the name anostrings.txt in the Fiji plugins directory.

You can place text at desired locations on the images for explaining some feature of interest. Clear Last and Clear All work the same as in Measure, in this case clearing the text. The box shows that 11 text strings are currently defined.

Bookmarks

This may be the most important of all the tabs in that you may decide what you want to show at a talk and use this to scroll through the slides of interest. Mark Slice is rarely used since any action with Measure, Arrows and Text will automatically bookmark the slice on which the action took place. Mark Slice could be used to mark an additional slice on which no annotations are defined.

Mark Slice changes to unMark Slice when you happen to be on a slice which is already marked. This allows you to remove it from the list of marked slices, as well as to know if this particular slice is marked or not.

Move down/up are what you would use in your talk to step through your predefined slices. Single Orientation means that if you are currently in the axial mode, don't scroll through bookmarks defined on the coronal or sagittal views. To see those, click on the coronal or sagittal icon and scroll through the chosen orientation slices.

Automatically switch to Bookmarks means that after you have switched to the Measure, Arrows or Text tab and have added an annotation, you will automatically be switched back to the Bookmarks tab. Why would you want this option? While you are in any of the above tabs any click on the screen will add a corresponding annotation. What you would prefer is to continue with your usual analysis where a click on the screen would give you an SUV value instead. Clicking on the Bookmarks tab allows you to continue with normal analysis.

Note that the bookmarks include not only all annotations but the chosen zoom and gray scale as well. In the example below a zoom of 6 has been used and the slice panned over to a corner. This uses the standard SUV=5 but if the slice was in the brain a SUV=10 could have been used. The bookmarks will scroll changing zoom and gray scale as defined when you prepared your talk.

Save

The 3 options are

• All objects exist in memory only - for use until the study is closed.
• Save all objects as a permanent part of the study.
• Delete all object from study.

This tab needs to be used only when you are preparing your talk. Then you will prepare all the slices of interest and choose Save all object as a permanent part of the study. If at some later point you add or delete objects and forget to choose to save the changes, then all the original objects will remain unchanged. They will remain in the changed state even if you close the annotations and reopen annotations, but if you close the study itself and reopen it, only the original objects will appear.

Thus the choice All objects exist in memory only is the default choice - there is no point to saving objects which haven't changed.

Delete all objects from study is used to erase the graphics files from the disk, permanently deleting them.

The actions take place when OK is pressed.