MRIOtl: step-by-step tutorial

1. Unpack the directories, and start matlab

unix: gunzip CTMRedit.tar.gz images.tar.gz; tar xvf CTMRedit.tar; tar xvf images.tar; matlab;

DOS/Windows: pkunzip -d CTMRedit.zip; pkunzip -d images.zip; matlab;

2. Add the CTMRedit directory to your matlab path

>> cd CTMRedit; path(pwd, path);

This is important. CTMRedit will change the current directory, so you will not be able to count on simply running commands in the current directory. If you want to remove files from your path after you have run the demo, you can use the "rmpath" command.

3. Mex the geread_i function, so it runs faster.

>> mex geread_i.c; (If you are using matlab 5.2, you can type "mcc geread_i.m" instead; the effect is pretty much the same).

4. Start CTMRedit, specifying the image directory as argument

The argument syntax is actually quite flexible; you can specify as much or as little of the path as you want, and CTMRedit will try to guess the rest. If CTMRedit guesses wrong, you can usually steer it to the right place using the popup menus.

>> cd ..

>> CTMRedit images/ae/a

The image window should come up looking something like this.

If some of the images are not found, you can usually load them by choosing the right path from the popup windows (see the visual guide).
If the images are too bright, you can darken them by pressing the "Dark" button next to the image you wish to darken.

CTMRedit window, with full-sized main image

5. Zoom in on the throat region

If "Zoom On" is selected from the tools list (or checked in the Tools menu), you can use the imagesm function to zoom without aliasing:

Zoom in with a left mouse click.
Zoom out with a right mouse click.
Zoom to a region by selecting it (left press and drag).
Move the window up, down, left, or right without zooming by shift-clicking on that side of the image.
Zoom all the way out by double-clicking, or by choosing "Original Size" from the list of tools.

CTMRedit window, with zoomed main image

6. Load the Distribution Outline

Press the "Loud Otl" button to load an outline from the distributed outline file (which is located in the directory images/ae/a/otl/).

CTMRedit window, with outline loaded from the
distribution

7. Clear the Distribution Outline

Delete all points in the displayed outline by pressing the "Delete All: Outline" button. Note that any changes to an outline (including "delete all points") do not affect the saved outline file until you save it. Don't save your empty outline right now; it's nice to leave the distribution outline where it is.

8. Create Your Own Outline using the Add Line Tool

Choose "Add Line" from the list of editing tools. Click to start the outline. Click again at each corner point.

CTMRedit window, in the process of adding a multiline

9. Complete the Add Line function by Double-Clicking.

When you're done with your outline, double-click on the last point. All of the lines will be converted into points.

CTMRedit window, multiline converted to outline points

10. Save Your Outline in a File

Place the cursor over the text "EdOut18," and click to get an I-bar text cursor.
Use normal typing commands (cursor, backspace, etc.) to change this text so that it contains some other file name.
If you type return, the filename will scroll off the top of the text box; type backspace to get it back (if you leave the return characters there, they will become part of the filename!!)
When you are done, press the "Save Otl" button to save your work.
Test your save: press "Delete All: Outline" to delete the outline points, then press "Load Outline" to bring them back.

11. Adjust the Intensity Threshold

If you adjust the "Threshold" slider, CTMRedit will use a red 'X' to mark every pixel at which the image intensity crosses the selected threshold.

CTMRedit window, showing threshold-crossing points

12. Use the Magic Wand Tool to Outline a Region

Once you have chosen a threshold value that you like, choose the "Magic Wand" tool, and left click in any dark region. After some computation, CTMRedit will outline the dark region with green points.

CTMRedit
window, region outlined using Magic Wand

13. Delete Unnecessary Points Using the Delete Tool

Delete all of the red 'X' marks by pressing the "Delete All: Thresh" button.
Choose the "Delete Points" tool. Press and drag the left mouse button (you will see a purple deletion rectangle) to select the points you wish to delete. Use this tool to delete all of the extraneous points which were generated by the "Magic Wand" tool.
Save your new outline in an otl file, possibly different from the one you chose previously.

CTMRedit window, outline cleaned up using Delete Points