MIPAV configuration files

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This section includes definitions and examples of the following files: preference, LAX, and Analyze.

Preference file

What is its purpose?

The preference file (mipav.preference) contains either the default or customized settings for running MIPAV. These settings determine whether some features appear or how certain features look.

You can customize the settings in the file by selecting Help > Program Options in the MIPAV window. For example, you can change whether the splash screen appears when you start the program, whether the scripting toolbar appears, the color of the crosshair cursor, whether the log mode is turn on, and so on.

When and how is it created?

MIPAV generates a preference file for all users when the program is run for the first time. Usually, the first settings recorded in the preference file are the memory setting, or maximum heap size, and the default image directory. When you first customize one or more of the settings in the Program Options dialog box, MIPAV adds those settings to the preference file as well as the default settings for those features you did not change. If you later make changes to those same preferences, the program adds those new settings to the preference file. In other words, the initial preference file is very small. It grows in size as you customize the program with the latest changes appearing last in the file.

Where is it stored?

By default, MIPAV stores the preference file in your home directory.

Table 4. Default home directories
For . . .
The home directory is . . .
Window users
C:\Documents and Settings\userID
Unix users

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MacIntosh users

However, if MIPAV is installed on a network and several users access it remotely, preference files are stored in the network home directory.

Note: The system administrator for the network may select another directory on the network in which to store proference files.
What does it look like?
An example of the preference file appears in Figure 4. For ease of discussion, line numbers appear on the left of each line in the figure, although they don't appear in the actual preference file.
Note: Your preference file may not have the same ordering of information as in Figure 4; as you customize MIPAV, your preference file changes to reflect the additional information.
Figure 4. Example of MIPAV.preference file

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# MIPAV preference file
#Mon Mar 19 15:12:48 EST 2001
LightBoxGridRow=2
LightBoxBorderSize=3
EnableDICOMReceiver=true
TRIM=0.4
DEBUG=true
PlugInFile3=SpreadSheet
PlugInFile2=GraphPanel
PlugInFile1=Chart
Swing=true
LightBoxRowDependant=true
PlugInView1=DrawTest
PlugInAlgorithm1=GraphApplet
Server1=MRIPS;MARS;137.187.26.152;104;
Storage1=MIPAV;MIPAV;C\:\\images;3100
SplashGraphics=no
LightBoxGridColor=000000
LightBoxBorderColor=960000
LightBoxGridSize=5
LightBoxMagnification=45.0
LightBoxGridCol=2
ImageDirectory=D\:\\Java\\jdk1.3\\demo\\applets\\SpreadSheet LightBoxLocation=813,23
1-2
Indicate the type of file and the date and time of the last update (comment lines).
3-4
Indicate default settings the light box image window.
5
Shows DICOM information and indicates whether the DICOM Receiver is on by default. If the DICOM Receiver is on, you can receive or retrieve DICOM image files.
6
Indicates the default trim parameter. The trim parameter is discussed in detail in Chapter 7.
7
Indicates whether MIPAV is placed in debug mode. If MIPAV is placed in debug mode and technical problems occur while you use the software, error messages are logged in the Output window.
11
Indicates whether the Swing-generated graphical user interface (GUI) is displayed. If the preference is set to false, the Advanced Windows Toolkit (AWT)-generated GUI appears instead.
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Indicates default settings the light box image window.
13-14
Shows plug-in file information.
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Shows DICOM information and shows hosts table entries. (The hosts table is located in the DICOM Communication Panel window.)
Line 15 shows the server (device) entry.
Line 16 shows a storage destination entry, which indicates where image files are stored when they are received or retrieved. If you indicate more than one storage destination entry, more lines appear in the preference file.
For more information on MIPAV`s DICOM capabilities, refer to [MIPAV_DicomImages.html#1259465 "Working with DICOM Images" on page 85].
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Shows DICOM information.
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Indicates whether an introductory splash screen appears when you start MIPAV.
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Indicates default settings the lightbox image window.
23
Shows the image directory.

MIPAV LaunchAnywhere executable (LAX) file

What is it and what is its purpose?

The LAX file is a LaunchAnywhere Executable (LAX) file that contains MIPAV's runtime environmental options. It may be helpful to access the file if you contacting the software developers during the debugging process. To contact MIPAV developers, use the MIPAV contact page.

LaunchAnywhere is a commercial program created by Macrovizion, Inc. and used to install and start the MIPAV software on your system.

The runtime environmental options in the LAX file are set during the development of the MIPAV software. If you install MIPAV on any Windows, UNIX, or MAC OS operating system, the LaunchAnywhere program copies a LaunchAnywhere Executable (LAX) file to the same directory as your other MIPAV software files.

Analyze files

Analyze formatted files are generated by a UNIX-based, image-processing application developed at the Mayo Clinic. In support of some NIH intramural researchers who have used Analyze in the past and have generated a large number of legacy datasets, MIPAV reads and writes Analyze formatted images.


An image file in Analyze format contains uncompressed voxel data for the images in one of several possible voxel formats:

1 bit packed binary (slices begin on byte boundaries)

8 bit unsigned char (grayscale unless .lkup file is present)

16 bit signed short

32 bit signed integers or float

24 bit RGB, 8 bits per channel

The header file is a C structure that describes the dimensions and properties of the voxel data.

Analyze images are formed from the following files:

Header file - This file (extension .HDR) describes the image type, size, and other important image attributes. For example, brain.hdr is the header file that describes the image file.

File Containing the Actual Image Data - This file (extension .IMG) can be interpreted as a raw file since it does not have any header information within the file. For example, brain.img is the file that contains the image data.

A color lookup file is sometimes included in the file set - A LKUP extension indicates a lookup table file. Example: file.lkup.

All files from the file set have the same name and are distinguished by the extensions HDR for the header file, IMG for image file and LKUP for lookup table file. MIPAV stores files in Analyze format in the catalog you specified in the Save Image as dialog box.

Note: MIPAV could save images with *.img extension either in Analyze format or in [#NiftiFormat NIFTI format]. To save an image in Analyze format, call the File > Save Image as menu, and then type the file name with *.img extension. In the Choose Type of File to Write dialog box that appears, specify the file format (Analyze). Check the option Always save .img files in Analyze format, if you want MIPAV to save .img files only in that format.


For more information about Analyze file format, please refer to the ANALYZE 7.5. format document from the Mayo Clinic.

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