Matlab integrates mathematical computing, visualization, and a powerful language to provide a flexible environment for technical computing.
- MATLAB also allows you to write series of commands into a file and execute the file as complete unit, like writing a function and calling it. MATLAB allows writing two kinds of program files − Scripts − script files are program files with.m extension. In these files, you write series of commands, which you want to execute.
- Double click on dcm2nii.exe - a file named dcm2nii.ini will be created. If you are using Windows, this file is in the same folder as dcm2nii. If you are using Unix (Linux, OSX) then this file is created in your home directory. (optional) Open dcm2nii.ini with a text editor (double click on the file.
MIJ is a java package to exchange images between MATLAB and ImageJ. It is written by Daniel Sage (Biomedical Image Group (BIG), Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland) and Dimiter Prodanov (Department of Physiology and Pharmacology, Université Catholique de Louvain (UCL), Brussels, Belgium). It allows to start a instance of ImageJ inside MATLAB and exchange images back and forth with it. It takes advantage of the fact that the user interface of MATLAB is written in Java.
For your convenience, Jacques Pecreaux & Johannes Schindelin wrote Miji.m, which makes it super-easy to use Fiji and the libraries and functions provided by Fiji's components from within MATLAB. Simply make sure that the scripts/ directory of your Fiji.app/ is in MATLAB's search patch, via File › Set Path... (on Mac, the file chooser doesn't let you choose directories within .app packages, so you have to use the MATLAB command addpath('/Applications/Fiji.app/scripts') ). Then a simple
will start a Fiji inside MATLAB.
- 1Getting started
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Using MATLAB as processing core and sending results to Fiji
An example how to work with MIJ is provided here:
If you get an error saying that some Plugin related classes cannot be found, please update your Fiji with Help › Update Fiji!
Running ImageJ commands
In ImageJ, you can record macros, one of the most powerful ways to use the program. Most of the recorded statements will look like this:
The first parameter to the run() method is the menu item's label which identifies the plugin to run (in this example, the label would read: Command).
The second parameter is a String containing values the user specified via an ImageJ dialog. Every value is identified by a label, and except for checkboxes (such as key2 in the example above), they have values. If the values contain spaces, you need to enclose the value in square brackets (such as key3 in the example above).
Note that the backslash is a so-called escape character, i.e. it can be used to insert special characters such as line breaks or tabs. To insert a plain backslash, it has to be repeated therefore (as in the key3 value: C:Documents and Settings becomes 'C:Documents and Settings').
You can use those recorded statements in a slightly modified form via MIJ:
- replace the double quotes by single quotes
- prefix the run name with MIJ.
The above example would read like this:
Note: in MATLAB, it is not strictly necessary to end the MIJ.run() statement with a semicolon, because it does not return anything. However, it is good practice with MIJ to end all statements in semicolons: some functions return images, cluttering the output and taking a very long time to print if the statement does not end in a semicolon.
Opening images
Normally, the best way to use MIJ is to use ImageJ's macro recorder. However, this procedure does not work when opening images because ImageJ records simply: open('/path/to/image.png');
Instead, one needs to keep in mind how run() statements are constructed and imitate it for the Open... command:
Using Fiji as a 3D viewer for MATLAB
A set of demos made for MATLAB users, and introducing how to install and use Fiji as a visualization tool for MATLAB is published on the fex.
To get a quick help on the available functions, call
Further descriptions and example code can be found on the home page for MIJ. Eventually, detailed documentation about the class MIJ can be found here (suitable if you have a bit of experience with Java).
If you want to use the functions without starting Fiji's graphical interface, just call
A related project is MatlabControl which allows you to start MATLAB conveniently from within Java.
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So far, we have used MATLAB environment as a calculator. However, MATLAB is also a powerful programming language, as well as an interactive computational environment.
In previous chapters, you have learned how to enter commands from the MATLAB command prompt. MATLAB also allows you to write series of commands into a file and execute the file as complete unit, like writing a function and calling it.
The M Files
MATLAB allows writing two kinds of program files −
Scripts − script files are program files with .m extension. In these files, you write series of commands, which you want to execute together. Scripts do not accept inputs and do not return any outputs. They operate on data in the workspace.
Functions − functions files are also program files with .m extension. Functions can accept inputs and return outputs. Internal variables are local to the function.
You can use the MATLAB editor or any other text editor to create your .mfiles. In this section, we will discuss the script files. A script file contains multiple sequential lines of MATLAB commands and function calls. You can run a script by typing its name at the command line.
Creating and Running Script File
To create scripts files, you need to use a text editor. You can open the MATLAB editor in two ways −
- Using the command prompt
- Using the IDE
If you are using the command prompt, type edit in the command prompt. This will open the editor. You can directly type edit and then the filename (with .m extension)
The above command will create the file in default MATLAB directory. If you want to store all program files in a specific folder, then you will have to provide the entire path.
Let us create a folder named progs. Type the following commands at the command prompt (>>) −
If you are creating the file for first time, MATLAB prompts you to confirm it. Click Yes.
Alternatively, if you are using the IDE, choose NEW -> Script. This also opens the editor and creates a file named Untitled. You can name and save the file after typing the code.
Type the following code in the editor −
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After creating and saving the file, you can run it in two ways −
Clicking the Run button on the editor window or
Just typing the filename (without extension) in the command prompt: >> prog1
The command window prompt displays the result −
Example
Create a script file, and type the following code −
When the above code is compiled and executed, it produces the following result −