Version 1

The plug-in is developed with the Java language version 1.3. It works with the software ImageJ that was created by the National Institute of Health (NIH). You can find this application at: http://rsb.info.nih.gov/ij/. ImageJ is in the public domain.

For the implementation we use a library that is under GPL license which name is itext version 1.3. This library allows us to export pdf reports. You can find it at: http://www.lowagie.com/iText/.

The MRU plug-in is free and can be downloaded by anybody. We decline any responsibility in its usage.

In order to use the plug-in you have first to download ImageJ software and install it.

Then, in the ImageJ plug-in folder, create a new folder.

Then, copy the jar file if you downloaded it,

Or copy the different files if you downloaded the zip file.

The main interface

The main interface is composed by different sections. Each section has its own role in the application and is independent from the others. So, you can use only the section you want.

Four sections are available (numbered 1-4 on the following image) as well as some helpful tools (at the bottom of the interface).

(1) – For renal excretion assessment

(2) – For renal function examination (volume and area can be used independently)

(3) – In order to collect information for the report

(4) – Image manager to capture images from the stack and manage them

Brightness/Contrast – Tool to improve the viewing (ImageJ tool)

Recal – Tool that allows image spatial adjustment

OK – Edits the report and closes the interface

The excretion assessment

The goal of this exam is to obtain the excretion curve for each kidney. We will explain here the way to reach this goal by studying the actions to do.

The first thing to do is to launch the application under ImageJ. Then on the main interface, you must click on the button “Right Kidney” or “Left Kidney”. If there is no opened Dicom stack, the program asks you to load one (if a stack is already opened, you directly get the manager). Choose a stack and the program opens it. You can see that the program is under processing from the following interface:

Then you obtain this one:

After this operation, you obtain two new windows. The first one is the image stack and the other one is the ROI manager (ROI: Region Of Interest) that allows you to analyze different ROIs by saving or loading them.

On the stack window, select an irregular ROI like in the following example. The ROI can surround either the entire kidney or the excretory system.

Then on the ROI manager, click on the button “add”. A dialog box asks you the name for the ROI you want to add to the list. Default one is an alternate choice. The ROI is added at the end of the Manager ROI list. You can add different ROIs and select the one you want by using the manager. Select the ROI you consider the best one to obtain the excretion curve, then click on the “MRUGraph” button.

The result of this action is a new window in which appears the “Excretion curve”.

Make these actions for each kidney to obtain the two different curves. You can keep the stack open and just click on the other button. You must close the MRUGraph window to trace another curve.

Split renal function

The goal of this exam is to evaluate the respective role of each kidney in the total renal function (split renal function). Different MR methods have been described. Some only compare the volume of the kidneys. Others use the area under the curve from basis level to glomerular peak (ROI of renal parenchyma - cortex plus medulla). At least, others use the association of both methods.

I) “Area under the curve”:

The principle is the same as the excretion one. Click on the button “Right Area” or “Left Area”. The ROI Manager appears directly if there is an opened stack. If not, you must open one, like before.

Once the stack is opened, you have to create a ROI with the ImageJ tools. This one must be limited to the parenchyma (cortex and medulla – excluding excretory system). You can see one on the following image:

Once your ROI is selected, add it to the ROI Manager list, then select it. Click on the MRUGraph button in order to get the graph window. At this moment you get an intensity curve representing the enhancement of the kidney.

By clicking on the “ZOOM” button, you can focus on the relevant part of the curve. This part begins at the minimum point after the vascular peak (P level) and ends with the maximum point (G for glomerular point) after the P level.

You can see the zoomed section and levels P and G on the next page.

We need now to compute the area under the curve limited by these points. Firstly click on the “evaluation” button. Click on the first point (P) and then on the second one (G). A new window appears to choose the interpolation type.

You can choose the solution you want (but you have to choose the same for the two kidneys!). You obtain a result that appears in the graph window and in the main interface.

Repeat these actions for the other kidney to get the area under the curve. Once you have got the area for the two kidneys, the main interface computes the kidney function (only from the area values).

You can see the result on the following image:

If you decide to modify manually the values, the application automatically computes the percentage.

II) Volume assessment:

A stack of approximately ten joint images (T1 weighted, Fat suppressed images) is necessary to assess the renal volume.

Click on the “Right Volume” or “Left Volume” button. This opens new windows if a stack is already opened. If no stack is opened, the program asks the user to open one and then open these windows.

The first one gives information drawn from the Dicom fields. The user must validate or modify the values. This information is used to compute the volume of the kidney in ml ³.

Now you can access to the volume manager that will help you to compute the volume from the image stack.

You have three solutions at this moment:

- First one is to select your own ROI and then click OK.

- Second one is to double click on the enhanced kidney (in the middle of the widest area possible because the segmentation tool uses the pixel neighborhood to compute the threshold values). You get an automatic segmentation of the kidney. You can adjust the ROI by using “+” and “-“ buttons in the two threshold sections.

- No kidney appears on a given image: click on the “No kidney” button.

You had to do that for each image. When you click on “OK” or “No kidney”, the image stack window jumps to next image.

You can see how it works with the following image on the next page.

When all images are segmented in the stack, the “compute” button becomes clickable and you have to click on it to get the result.

Before computing, if you want to verify the different selections, you can do it by using the stack window scrollbar. The different regions of interest are saved in the application so you can adjust or modify them.

Repeat all these actions with the other kidney to get volume for the two kidneys. Once you get the volume for the two kidneys, the main interface computes the kidney function (only with the volume values if there are not valid area values).

III) With the area under the curve and the volume:

To compute the kidney function with the area and the volume, you had to follow the stage I and II. The main interface will compute the result with all the values given.

The application verifies if the values are valid. If not, the application computes the result with the valid couple of values. If there are no valid values, a status message appears.

The information section

Type the indication (kind of disease) in the indication section. Type the findings in the diagnosis section.

The image manager

The image manager is a part of the main interface that allows the user to add images to the report. The manager is easy to use.

There are three buttons in this manager. The first one is the “Store” button that allows the user to add an image to the report. The second one is the “Delete” button to remove the selected image from the images list. The last button (Comment) is useful to add or modify a comment to a selected image.

I) Store an image:

When you want to add an image to the report, you must click on the “Store” button in the image manager. Beforehand, an image stack must have been opened. When you click on this button at the first time, the application asks you to indicate a folder in which you want to save this image. This folder will be the same for the report and the other images so we advise you to create a new one for any new patient.

Get into the folder, then click on “Save”.

A new window appears directly to add a comment to this image. The comment will appear in the report under the image like a caption.

Write your comment, then click on the “OK” button to validate this operation. You can let a blank comment. It will be possible to modify it afterwards. Your image appears with the name image + number in the list.

You can repeat this operation without any limitation.

This method allows the user to capture images with or without ROIs from the Dicom image stack.

It is also possible to add curves to the report.

When you get a graph in the MRUGraph window, you can easily add it to the report images list by clicking on the “Save Graphics” button from the MRUGraph interface. According to the study you made, the image will take the name “RightExcretionCurve”, “LeftExcretionCurve”, “RightAreaCurve” or “LeftAreaCurve”.

Note that you can only save one curve by type. If you compute a second curve for the same examination, it will erase the old image.

The image name appears in the images list and a default comment related to the image is included (modifiable).

Note:

- The examination type is indicated in the title of the ROI Manager window

- You can watch an image by double clicking on it in the images list

II) Delete an image:

To delete an image and its comment, select the image in the list, then click on the “Delete” button.

III) Add/Modify a comment:

To modify your comment, select an image, then click on the “Comment” button. A new window appears with the comment associated to the image.

Then, write the new comment in the field and validate the change.

Main interface – Other features

I) Brightness/Contrast:

This button opens a window that allows the user to modify the Brightness and Contrast of the image stack. This window is an ImageJ window.

First click on the “Auto” button. The result is usually good.

II) Recal:

Due to the breathing movement, the kidney can be in different locations from an image to another while the ROI is the same for the entire stack.

We created a tool that moves the image of the stack in order to re place the ROI around the kidney (we must precise that the kidney shape does not change at all, it only moves with the breathing movement).

Click on the different buttons to move the image in order to set the ROI around the kidney.

III) OK:

The “OK” button creates the report in two formats (html and pdf). When you click on this button, the files are created and saved. Then the interface is closed.

Some information is added to the report like the patient last name, first name, examination date and type… This information is withdrawn from the Dicom image fields in the stack.

The file in html format is like that:

If you want to print the report, the page may cut an image between two pages. In such case, print the pdf file.

The pdf file is like that:

Plug-in - Other features

Many other advanced features are not useful for basic use. They are described thereafter.

I) Volume configuration:

You can set the segmentation parameters in the volume manager. Click in menu, then in option. You obtain the following window.

Space: the space between two points of the ROI

Smoothing: for the Gaussian blur

Opening and closing: for the value of the erosion and dilatation

II) Save a ROI and an exam:

You can save a ROI or an examination by clicking on the “save ROI” or the “save Exam” button in the ROI manager window.

III) Save the Graph point value:

To save the numeric points of the graph, you just have to click on “yes” when leaving the MRUGraph window.

IV) Get the stack information:

To get the stack information you just have to click on the “stack Info …” button in the MRUGraph window. You can add information to this section, but only when you open a stack.

When you open a stack, you obtain the following window:

Click on the “Info…” button. You obtain a new window.

To add information, click on a line in the left section and then click on the “->” button. When you finish, click on “OK”.

When you click on the “stack info …” button in the MRUGraph window you get the following window:

V) Change the graph option:

It is possible to change the scale of the graph in the MRUGraph window. You just have to click on the “Graph Options” button and then modify the value in the following window. Evaluation only works when the scale is in seconds.

Advice to avoid problems

- Open only one stack at the same time

- Open the stack with the plug-in (we keep information when opening it)

- Never put different stacks in the same repertory

- Respect the Dicom fields

- Follow the preceding instructions

- And read good articles :)