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3. Starting and Running BioImage Suite

3.1 Installation Overview

Installing BioImage Suite is a relatively simple process. On Microsoft Windows, we provide a self-contained installer file that completely automates the procedure. On UNIX derivatives (this includes Linux and the Apple Macintosh Operating System) the procedure involves uncompressing four files in the /usr/local directory or another location of your choice (in which some script files may need to be edited.)

3.1.0.0.1 Overview: What is included:

All files required for BioImage Suite are available from the BioImage Suite webpage - www.bioimagesuite.org. Special effort is made to package almost all required packages/libraries with the system ^3.1

BioImage Suite consists of four parts (which are collapsed into one file in the case of the Windows Installer):

1. A pre-compiled binary itk241_yale distribution containing the Insight Toolkit (ITK) v 2.4.1.
2. A combo binary vtk44_yale distribution which contains the Tcl/Tk scripting language, various Tcl extensions and the Visualization Toolkit. This includes binary versions of:
   1. The Tcl/Tk scripting language version 8.4.11
   2. The following Tcl/Tk Extensions:
      • Incr Tcl 3.2.1
      • tcllib 1.8.1
      • IWidgets 4.0.1
   3. The CLapack numerical library v3.
   4. A slightly patched version of the Visualization Toolkit with TCL Wrapping (v 4.4.2)
3. A pre-compiled bioimagesuite_extra distribution^3.2 consisting of the MINC 2.0.11 distribution and Xercesc 5.7.
4. Installation of the BioImage Suite software package itself.

3.2 Installation Instructions

For BioImage Suite 2.6, we have two types of installers: Complete and Update. The ``Complete'' installer is a self-contained installer that installs BioImage Suite and all the required software in the specified directory. The ``Update'' installer assumes that you have previously installed BioImage Suite 2.5 and updates the files in the ``bioimagesuite'' directory. NOTE: If upgrading, it is crucial that you install BioImage Suite in the same directory where you have previously installed BioImage Suite 2.5. In the case on Windows, the directory will most like be C:$\backslash$yale and in the case of Linux/Mac, the directory will mostly like be $\backslash$usr$\backslash$local. Please confirm the existence of BioImage Suite in these directories before updating it.

3.2.1 Microsoft Windows

Figure 3.1: The Windows Installer in Action. The default location is C:/yale. Please avoid locations with spaces in the directory names - e.g. C:/Program Files !

For Windows, there are two distributions: ``vs2003'' and ``vs2005''. The ``vs2003'' version is compiled for users who use an older version of Windows such as Windows 2000 etc. The ``vs2005'' version is complied for users using Windows Vista/XP. Once you have selected the distribution and the kind of installers (Complete/Update), simple download and execute the all-in-one installer to install BioImage Suite. - this is shown in Figure 3.1. The installer will ask a couple of questions and then perform the installation. The default and recommended installation directory is c:/yale. Please avoid installing BioImage Suite or storing data in directories containing spaces in their names - including unfortunately defaults such as ``Program Files'' and ``Documents and Settings'' - mercifully this later convention is eliminated in Microsoft VISTA.

Figure 3.2: The BioImage Suite entry in the ``Start'' menu in Windows Vista. Identify the BioImage Suite entry in the menu and click on ``BioImage Suite Console'' or ``BioImage Suite Menu'' to start BioImage Suite.

Once the installation is complete an entry in the Start Menu appears (see Figure 3.2). The key entries are the BioImage Suite Menu which launches the main application, as in Figure 3.3 and the BioImage Suite Console which is a special command prompt that allows for the running of commandline applications etc.

3.2.2 UNIX: Linux and Mac OS X 10.4

The installation for both of these systems is now as simple as running a single ``.sh'' file.

3.2.2.0.1 Downloading the appropriate installer

The user should identify the type of installer that the user wishes to install. For example, if the user prefers to download a ``complete'' installer compiled using ``g++-4.0'' for ``Linux'' on a 32-bit machine, the user would download the following file:

 bioimagesuite-26_beta1_15_Jul_2008-Linux-g++-4.0-i386-complete.sh

. In case, the user were downloading an ``update'' installer compiled with ``g++34'' for a 64-bit ``Linux'' machine, the file to be downloaded would be

bioimagesuite-26_beta1_15_Jul_2008-Linux-g++34-x86_64.sh

3.2.2.0.2 Installing

To install BioImage Suite, type

• sh ./bioimagesuite_[filename].sh
  

  where [filename] should be replaced with the kind of file that you downloaded as described above. On Mac, you may have to type

   sudo sh ./bioimagesuite_[filename].sh --prefix=/usr/local
  

• Answer ``Yes'' to the question asked.
• On Linux, Menu Entries for GNOME and KDE can be created by typing
  bioimagesuite26/createmenuentries.sh.

To start BioImage Suite (on Linux/Mac), type

path/bioimagesuite26/start_bioimagesuite

NOTE: Here ``path'' should be replaced with /usr/localor the specific path that you may have specified during installation.

Figure 3.3: The BioImage Suite Start Menu entry. Pressing the ``?'' button next to each application shows how to directly invoke it on the commandline.

Alternatively, you could start the BioImage Suite console by typing:

path/bioimagesuite26/bis_console

or use the Menu Icons in Applications/Other (which are created if createmenuentries.sh has been executed as specified in the ``Installing'' section above).

3.2.2.0.3 Note:

BioImage Suite, unlike many other software packages, uses accelerated 3D Graphics. This has two implications: (i) The quality of the graphics card is important - ideally you will need a decent video card (much like for games!) from somebody with like an NVIDIA chipset (recommended) or ATI - with properly configured drivers (on Linux you can use the `glxgears' program to test this. (ii) Remote display of BioImage Suite, i.e. running on one machine and using the X-window protocol to display on another, will result in a significant performance hit - especially if volume rendering is involved. A BioImage Suite installation needs about 300 MB of disk space.

3.3 The Main BioImage Suite Menu

There is no such thing as the BioImage Suite application program. Rather, BioImage Suite consists of a number of different utilities/applications which share a number of common controls/elements. Depending on the task at hand, one needs to select the appropriate application. The following snapshots are all taken on a Windows Vista computer, however the appearance on other platforms is very similar.

The BioImage Suite main menu application, which is shown in Figure 3.3, consists of a tab-noteboook which contains launch buttons for the various applications. We detail the applications next. In addition, the BioImage Suite ``Preferences Editor'' can be invoked using the ``Preferences'' button on the bottom button bar.

The BioImage Suite applications are grouped into seven groups namely:

• General - contains the core applications which are primarily geared towards neuroimage analysis, including Registration tools and tools for the formation of Multisubject Composite Functional Maps.
• DTI/Angiography - includes tools for diffusion weighted image analysis and early versions of our angiography tools.
• fMRI - includes the main functional MRI analysis tool and a GUI-editor for creating .xml files needed by this.
• Editors - contains the SurfaceEditor tool which allows for interactive segmentation of 3D images and surfaces. Two new applications the Mosaic Objectmap Editor and the Orthogonal Objectmap Editor provide functionality for ``painting'' objectmaps (i.e. manual segmentation) in multiple slices simultaneously. In addition, our specialized Electrode Editor - used for locating intracranial electrodes from CT images, is also available from this tab.
• Cardiac - has two tools for viewing and surface editing (variations on other tools) specifically adapted to 4D Image Analysis.
• Data Tree - accesses the new datatree tool which serves as a database-like front-end for BioImage Suite. A lot of the future growth of BioImage Suite will involve this functionality.
• Mousesuite - includes early versions of our segmentation/registration Mouse Tools specifically adapted for small animal imaging.

3.4 Preferences Editor

Figure 3.4: The BioImage Suite Preferences Editor.

The User Preferences Editor enables the setting of global parameters used by the BioImage Suite Applications. The preferences are stored in a file called .bioimagesuite in the user's home directory (in this case /agrino/xenios/.bioimagesuite as the dialog itself informs the user). Changes made in the ``Preferences Editor'' - which is also accessible under the Help menu in many applications only take effect once the application is restarted.

There are six tabs in the editor each containing different sets of options described below:

1. Look & Feel
   • Color Scheme - chose between System Default, BioImage Suite Blue, Bisque and High Contrast color schemes. See Figure 3.5 for an example.
   • Font Selection - sets the font for the menus/dialog boxes
   • Mirror Console - by default in most GUI applications most ``print-outs'' go to the BioImage Suite Console (accessible under Help/Console in most applications). Setting Mirror to 1 also sends any printouts to the native console (e.g. the DOS Window or the xterm window from which the application was started.

2. File Formats
   • Force Output Format - BioImage Suite automatically saves images either as Analyze or NIFTI depending on the input image. Set this to force the output image type.
   • Default Import Mode - sets the default import format for the Image Import Tool
   • Minc Image Format enables the use of the .mnc format (This is MINC2 which is not to be confused which the more commonly used MINC1 .mnc format).
3. Coordinates
   • ManualTalairach - set this to OFF unless you really know what you are doing!
   • YaleAtlasAutoInitialize - this setting can allow the Yale Atlas Tool to be automatically initialized, when needed.
   • WFUAtlasAutoInitialize - this setting can allow the WFU Atlas Tool to be automatically initialized, when needed.
4. Image Display
   • NormalizeAnatomical - If enabled, the default windowing used for image display is automatically adjusted to improve the contrast (Also available using the ``Nr'' Colormap in the Viewers)
   • Image Colormaps - if enabled, the current colormap is saved  upon saving the image and reloaded afterwards. This is also work in progress.
   • Interpolation - default interpolation mode for image reslicing.
   • Volume Texture Mode - by default, the software will use hardware accelerated volume rendering. Disable on systems with older graphics cards ($>$5 years old - any recent ATI/Nvidia card should work fine with this on)
   • FMRI Mode - selection of default colormap for overlay of functional images (these three choices are also available from the Overlay Tool).

5. Surface Editing
   • MaxSurfaces  - maximum number of surfaces available. Set this to the minimum requirement to speed up the application.
   • ControlPointSize - sets the default size of the control points in the spline editor.

6. Advanced/Miscellaneous
   • RigidRegistration - do not touch this unless specifically instructed to do so.
   • VectorVisionLink - enables the VectorVisionLink interface to the BrainLAB Vector Vision Cranial Image Guided navigation system.
   • Enable Beta Features - if on, additional options may be available which are considered experimental for now. Keep this off.

Figure 3.5: Changing the Color Scheme. Left: System (Default) Colors. Right: BioImage Suite ``Blue'' Color Scheme.

Webpage design by Marcello DiStasio.


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