ITK/FAQ

General information and availability

Do I need FLTK to build ITK ?

No,

ITK does not require FLTK. FLTK is only used in particular demo applications in the InsightApplications directory.

ITK does not provide any GUI functionality. When building full applications, the GUI is provided by other libraries such as Qt (http://www.trolltech.com/products/qt/index.html), FLTK (http://www.fltk.org/) Gtk+ (http://www.gtk.org/) or wxWidgets (http://www.wxwidgets.org/, which used to be called wxWindows).

If you want to build the demo applications that require FLTK, you must install FLTK in your system. The recommended version is 1.1.6 that can be obtained from ftp.fltk.org and from the "RelatedSoftware" page in www.itk.org.

Once FLTK is installed in your system, you will have to enable the USE_FLTK option when you run CMake to configure InsightApplications.

Do I need VTK to build ITK ?

No,

ITK does not require VTK.

VTK is only used by specific demo applications in the Insight/Applications directory. These applications will simply not be build if VTK is not available in your system.

ITK does not provide any visualization functionalities. Applications requiring visualization should implement those functionalities from internal code or libraries like OpenGL, GLUT or VTK.

In order to use ITK with VTK you must build VTK from sources and make sure that it is configured with the flag USE_ANSI_STDLIB enabled.

Then you have to reconfigure ITK making sure that the option USE_VTK is enabled.

Do I need GLUT/OpenGL to build ITK

No,

ITK does not depend on GLUT not OpenGL.

GLUT and OpenGL are only used by specific demo applications in the Insight/Applications directory.

ITK does not provide any visualization functionalities. Applications requiring visualization should obtain these services from external libraries like OpenGL, GLUT or VTK.

Do I need Tcl to build ITK

No,

ITK does not depend on Tcl.

However, there are three ways in which ITK is related to Tcl:

1. The testing system used by ITK dashboard is managed by Dart which is writen mostly in Tcl. If you want to configure experimental, continuous or nightly builds in your system using Dart. You will need Tcl installed.
2. ITK can be wrapped in order to be used from Tcl.
   This is done using "Cable". That gives ITK the versatility needed for developing rapid prototyping, and facilitating interactive teaching and experimentaion with ITK classes.
3. Some demo applications in the Insight/Applications directory have configured their visualization by using VTK. These demo-applications have packaged ITK filters inside VTK filters and then wrapped those into Tcl using the traditional Tcl wrapping mechanism of VTK.

What version of FLTK is required by ITK demo applications

The recommended version of fltk is 1.1.6.

The sources can be obtained from ftp.fltk.org

       ftp://ftp.fltk.org/pub/fltk/1.1.6/

or from the "Related Software" page in www.itk.org.

FLTK is not needed for building ITK itself. FLTK is only used by some of the demo applications distributed in InsightApplications

FLTK is in continuous development and it has been quite difficult to keep track of its configuration changes.

Also note that InsightApplications is not any more part of the core Insight Toolkit but is a standalone package.

What additional packages are required by each demo-application

The following list rapidly summarizes the additional pacakges required by demo applications in the Insight/Applications directory.

The following applications require VTK wrapped for Tcl. These applications insert ITK filters into VTK objects and then wrapp them to be used from Tcl.

• MRIRegistration
• SegmentationEditor
• vtkITK

This wrapping is done with the traditional VTK wrapping mechanism which is totally independdent of ITK mechanism based on Cable.

FLTK is used in the following demo applications to implement their GUI. The recommended version can be downloaded from http://www.itk.org/HTML/DownloadRelatedSoftware.htm

• DistanceMapFilter
• DicomImageViewer
• GaussianFilter
• GradientRecursiveGaussianFilter
• Curves2DExtractor
• Morphogenesis
• MutualInformationEuler2DRegistration
• ImageRegistration
• ImageRegistration2D
• RawImageReaderViewer
• RegionGrowingSegmentation
• ThresholdSegmentationLevelSet
• FastMarchingLevelSet
• ShapeDetectionLevelSet
• MetaImageViewer
• MetaImageColorViewer
• SurfaceGenerator

Among the applications using FLTK for GUI, the following applications also require VTK for visualizing segmented images in 3D:

• RegionGrowingSegmentation
• ThresholdSegmentationLevelSet
• FastMarchingLevelSet
• ShapeDetectionLevelSet

There is also an example of how to use Qt for GUI along with ITK:

• QtITK

What 3D file formats can ITK import and export?

The following table identifies the file formats that ITK can read/write via a factory mechanism based on the file extension (itk::ImageIOFactory). Some proprietary files format are only imported. More information on ITK File Formats is available, including data types supported.

A very nice tool for viewing all of these images is ImageViewer which can be found in the InsightApplication package (fltk is required).

File Format	Read/Write	Import
Analyze 7.5	AnalyzeImageIO
BMP †	BMPImageIO
DICOM	GDCMImageIO	Using DicomImageIO is backward compatible, but user should prefer GDCMImageIO
GE 4x		GE4ImageIO
GE 5x		GE5ImageIO
GE Advantage Windows		GEAdwImageIO
Gipl (.gipl)	GiplImageIO
IPLCommon		IPLCommonImageIO
JPEG †	JPEGImageIO
MetaImage (.mha/.mhd)	MetaImageIO
PNG †	PNGImageIO
Raw ‡	RawImageIO
Siemens Vision		SiemensVisionImageIO
Stimulate (spr/sdt)	StimulateImageIO
TIFF	TIFFImageIO
VTK Structured Points	VTKImageIO

† BMP, PNG and JPEG are not very good formats for 3D medical images. They only support 2D images and a limited set of pixel types such as unsigned char, and unsigned short. The great advantage of BMP, PNG and JPEG is that you can view them with almost any image viewer. It is possible to read/write 3D datasets as collections of 2D slices each one in an independent BMP, PNG or JPEG file by using the ImageSerierReader and ImageSeriesWriter.

‡ It is higly recommended not using this format. RAW is not a format, it is insufficient, inconsistent and simply dangerous. A RAW file without a header is useless, and once you add a header, it is not RAW anymore.

What if my file format is not supported by ITK ?

If ITK doesn't have a specific file format reader at this point.

You may try converting this specific file format image to a format like PNG, for which ITK has readers.

A good set of tools for performing such conversions is available in ImageMagick. It can be downloaded it for free from: http://www.imagemagick.org/

You can also take advantage of the VTK readers/importers. All you need is then use the VTKImageToImage adaptor in order to convert the vtkImageData into an itk::Image.

Supported VTK file formats can be found here: What image file formats can VTK read and write? and What 3D file formats can VTK import and export

How to read a volume from a DICOM series

The following are alternative options for reading DICOM series. The first one in the list is the recommended option. The others are provided in case of desperation.

1. Use the itk::ImageSeriesReader<> in combination with the DicomSeriesFileNames<>. For a full example on how to do this, please look at the source code under Insight/Code/Examples/IO/DicomSeriesReadImageWrite.cxx.
2. Write a MetaImageHeader
   This is a small text file holding information about the image: spacing, dimensions, pixelt type... This header can hold the list of dicom files you want to read. The only restriction is that the files must be uncompressed.
   The easy way to create a MetaImage header is to use the application: MetaImageImporter that is available in: InsightApplications/MetaImageImporter. you can also take an existing metaimage reader and modify it in order to fit your needs. Please find attached one file that you can edit it with your favorite text editor.
3. Use MRIConvert
   Jolinda Smith from the Lewis Center for Neuroimaging at the University of Oregon has developed a nice application that allows you to load DICOM series and export them in MetaImage and Analyze format (among others).
   She graciously has made this application publicly available at: http://lcni.uoregon.edu/~jolinda/MRIConvert There is a fresh version updated in april 14th.
4. Jeff Brubaker and Stephen R. Aylward, at the UNC
   CADDLab developed a DICOM query/move application called "MIND" (whit the motto: "MIND is not DICOM"). This application loads DICOM files over the network and export them in MetaImage format. This application is open source and it is available at: http://www.jeffro.net/mind/ and http://caddlab.rad.unc.edu/software/MIND/

How to write a volume as DICOM series

Use ITK in combination with gdcm

http://www.creatis.insa-lyon.fr/Public/Gdcm/

GDCM is an open source package developed by the Creatis team at INSA-Lyon. It is distributed under a license similar to ITK.

http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html

GCDM uses CMake in order to configure its build process, so you will find a familiar setup. Once you download, configure and buid GDCM, you can reconfigure ITK by running CMake in your ITK build, going into the Advanced options and enabling USE_GDCM.

For a code example on how to use GDCM for reading and writing DICOM series, please refer to the source code in

Insight/Examples/IO/DicomSeriesReadImageWrite2.cxx

UPDATE: As of ITK 2.4 this option: USE_GDCM has disapear since GDCM is now the default toolkit for reading DICOM image. See also Proposals:Make_GDCM_the_default_DICOM.

Interpreted languages supported by ITK

Currently ITK supports the following language bindings:

• Tcl
• Python
• Java

Java was added in February 2004, it will not be found in the ITK release 1.6. You will need a CVS checkout with a data posterior to February 25 2004.

How do I cite the use of ITK in a publication?

The Insight software may be cited by referencing the paper, the books, and/or the web site.

A) The paper:

T.S. Yoo, M. J. Ackerman, W. E. Lorensen, W. Schroeder, V. Chalana, S. Aylward, D. Metaxes, R. Whitaker. Engineering and Algorithm Design for an Image Processing API: A Technical Report on ITK - The Insight Toolkit. In Proc. of Medicine Meets Virtual Reality, J. Westwood, ed., IOS Press Amsterdam pp 586-592 (2002).

B) The books:

"Insight into Images"
 edited by Terry Yoo
 published by A.K. Peters 2004
 ISBN: 1-56881-217-5

"The ITK Software Guide"
 Second Edition
 Ibanez, Schroeder, Ng, Cates.
 published by Kitware Inc.
 2005
 ISBN: 1-930934-15-7

"The ITK Software Guide"
 First Edition
 Ibanez, Schroeder, Ng, Cates.
 published by Kitware Inc.
 2003
 ISBN: 1-930934-10-6

"Mastering CMake,
 A Cross-Platform Build System"
 K. Martin and B. Hoffman
 published by Kitware Inc.
 ISBN:  1-930934-09-2

BiBtex citations

 @Manual{ITKSoftwareGuide,
   Title          = {The {ITK} {S}oftware {G}uide},
   Author         = {Ibanez, L. and Schroeder, W. and Ng, L. and Cates, J.},
   Organization   = "Kitware, Inc. ISBN 1-930934-10-6",
   Address        = {http://www.itk.org/ItkSoftwareGuide.pdf},
   Edition        = {First},
   year           = {2003}
   }

 @Manual{ITKSoftwareGuideSecondEdition,
   Title          = {The {ITK} {S}oftware {G}uide},
   Author         = {Ibanez, L. and Schroeder, W. and Ng, L. and Cates, J.},
   Organization   = "Kitware, Inc. ISBN 1-930934-15-7",
   Address        = {http://www.itk.org/ItkSoftwareGuide.pdf},
   Edition        = {Second},
   year           = {2005}
   }

C) The Web sites:

"The Insight Segmentation and Registration Toolkit"
 www.itk.org

"CMake: Cross Platform Make"
 www.cmake.org

If you want to include ITK in an acknowledment section, a phrase similar to the following may be used:

"This work benefited from the use of the Insight Segmentation
 and Registration Toolkit (ITK), an open source software
 developed as an initiative of the U.S. National Library
 of Medicine and available at www.itk.org."

and

"The multi-platform configuration tool CMake was used for
 configuring ITK and facilitating its use from our project.
 CMake was partially funded by the U.S. National Library of
 Medicine as part of the Insight Toolkit project. CMake is an 
 open source system and it is freely available at www.cmake.org."

I got the message: "Could not create IO object for file"

Question:

When trying to read or write a file using the ImageFileReader or the ImageFileWriter I got an exception with the following message:

itk::ImageFileReaderException (00F7F494)
Location: "Unknown"
File: C:\ITK\InsightToolkit-1.6.0\Code\IO\itkImageFileReader.txx
Line: 101
Description: Could not create IO object for file c:\t1.mnc

What is going wrong ?

Answer:

This exception is thrown when ITK does not recognize the fileformat that you are trying to read or write. When reading, ITK recognize file formats by asking a set of internal readers to attempt to read your file. If none of the registered readers accept your file, then the exception above is thrown. When writing, ITK uses the extension of the filename in order to chose the fileformat to be used. You must make sure that you use one of the filename extensions recognized by ITK. Please look at FAQ entry 1.7 for a full list of those extensions and associated fileformats.

Additional details on the ITK Input/Output architecture are available in the ITK Software Guide: http://www.itk.org/ItkSoftwareGuide.pdf.

Is ITK FDA-Approved ?

Question:

 Has the Insight Toolkit been FDA approved? 

Answer:

Given the fact that ITK is a software toolkit, it cannot be the subject of FDA approval as a medical device. We have discussed this topic in several occasions and received advice from FDA representatives, that can be summarized as follow:

 ITK is to be considered as an off-the-shelf (OTS) product that
 is used for supporting a higher level medical application/product.
 The developer of such application/product will be responsible for
 performing the validation processes described in FDA published
 guidelines for the development of software-related medical devices.

For mode details see the page FDA Guidelines for Software Developement

Language bindings

Error opening hint file NOTFOUND

When you enable "USE_VTK" in the CMake configuration of ITK, and VTK was built with wrapping, CMake looks for a "hints" file.

The "hints" file is on the VTK source tree under: VTK/Wrapping/hints

Please switch CMake to "advanced", look for the VTK_WRAP_HINTS variable and set it to the full path to the "hints" file including the "hints" filename itself.

here is how it looks in the CMakeCache.txt of a typical ITK installation:

//Where can the hints file be found
VTK_WRAP_HINTS:FILEPATH=/home/johndoe/src/VTK/Wrapping/hints

How to use ITK with WrapITK

Please refer to the following article

http://voxel.jouy.inra.fr/darcs/contrib-itk/WrapITK/WrapITK_-_Enhanced_languages_support_for_the_Insight_Toolkit.pdf

It describes how to use WrapITK

Using Insight

How to combine ITK and VTK in my application

A full tutorial on how to combine ITK and VTK is available at

"Getting Started with ITK and VTK" http://www.itk.org/CourseWare/Training/GettingStarted-II.pdf

You will need the auxiliary classes available at

 InsightApplications/Auxiliary/vtk

For example, for converting ITK images into VTK images and back, you will find useful the files

     itkImageToVTKImageFilter.h
     itkImageToVTKImageFilter.txx
     itkVTKImageToImageFilter.h
     itkVTKImageToImageFilter.txx

Simply copy those files into the source code directory of your project.

For the full list of tutorials please look at

   http://www.itk.org/HTML/Tutorials.htm

Compile/Link errors involving C++ streams library

Compile and link errors involving the C++ streams library (ostream, istream, ifstream, ofstream, etc.) are usually the result of collisions between the old and new streams library. The C++ streams library in the Standard Library is different and usually imcompatible with the original C++ streams library. The new streams library is share the same class names as the old streams library but has a very different implementation (templates, thread safety, etc.). ITK can only be built using the Standard Library streams library.

If the compile/link error is in an ITK file, the solution is usually to include the proper stream header file, i.e. <fstream> before any other include file. The forces the streams library used by all subsequent headers to be the Standard Library version.

If the compile/link error is in an application that is trying to use ITK, the solution is usually to include an ITK header file before any other include file. This forces whatever include files that the application may use to use the Standard Library streams library.

What is the difference between the CMake options ITK_WRAP_TCL and VTKITK_WRAP_TCL ?

ITK_WRAP_TCL enables the official method of wrapping ITK into Tcl. This wrapping requires the installation of two external packages: Cable and GCC_XML. Information about these packages can be found at http://public.kitware.com/Cable/HTML/Index.html and http://www.gccxml.org/HTML/Index.html

VTKITK_WRAP_TCL is not really part of ITK. It is only required to enable the build of some demo-applications in the Insight/Applications directory. These applications use VTK for visualization. ITK filter are packaged here inside VTK classes that are subsequently wrapped for Tcl using the traditional VTK wrapping mechanism (not Cable).

EMACS configuration file : ITK coding style

You can add the following codes into your .emacs file

;;;;;;;;;;;;;;
(c-add-style "itk"
            '("stroustrup" 
              (c-basic-offset . 2)
              (c-offsets-alist
                (c . c-lineup-dont-change)
                (innamespace . 0)
                (inline-open . 0) 
                (substatement-open . +)
                (statement-block-intro . 0) ) ) )
(add-hook 'c++-mode-hook (function (lambda ()
 (c-set-style "itk")(turn-on-auto-fill))))
(add-to-list 'auto-mode-alist '("\\.txx\\'" . c++-mode)) (add-to-list 'auto-mode-alist '("\\.h\\'" . c++-mode))
;;;;;;;;;;;

VIM configuration file : ITK coding style

for all of you who use VIM, here are just couple of things:

set tabstop=2 " Tabs are two characters
set shiftwidth=2 " Indents are two charactes too
set expandtab " Do not use tabs
set matchpairs+=<:> " To mach arguments of templates
set cinoptions={1s,:0,l1,g0,c0,(0,(s,m1 " ITK/VTK style indenting

Then you can also use CMake indentation and syntax file which are available on www.vim.org.

This was contributed by Andy Cedilnik @kitware.com

FLTK_WRAP_UI called with FLTK_WARP_UI undefined

I use CMake to build the InsightApplications and the following error appears:

CMake Error: Error in cmake code at
../../CMakeLists.txt:20:
FLTK_WRAP_UI called with FLTK_WARP_UI undefined

I wonder where and how to define it.

This error message

"...FLTK_WARP_UI undefined"

appears when you have missed to specify some of the FTLK components.

Please run Cmake again, pass to "Advanced" mode and double check that you provided the right paths for the following components

• FLTK_BASE_LIBRARY
• FLTK_FLUID_EXECUTABLE
• FLTK_FORMS_LIBRARY
• FLTK_GL_LIBRARY
• FLTK_INCLUDE_DIR

Here is for example how they look in a typical Windows installation:

FLTK_BASE_LIBRARY       C:/cygwin/home/ibanez/src/fltk-1.1.4/lib/fltkd.lib
FLTK_FLUID_EXECUTABLE   C:/cygwin/home/ibanez/src/fltk-1.1.4/fluid/fluidd.exe
FLTK_FORMS_LIBRARY      C:/cygwin/home/ibanez/src/fltk-1.1.4/lib/fltkformsd.lib
FLTK_GL_LIBRARY         C:/cygwin/home/ibanez/src/fltk-1.1.4/lib/fltkgld.lib
FLTK_IMAGES_LIBRARY     C:/cygwin/home/ibanez/src/fltk-1.1.4/lib/fltkimagesd.lib
FLTK_INCLUDE_DIR        C:/cygwin/home/ibanez/src/fltk-1.1.4

Here is an example for a Linux installation

FLTK_BASE_LIBRARY       /home/ibanez/local/lib/fltk.a
FLTK_FLUID_EXECUTABLE   /home/ibanez/local/bin/fluid
FLTK_FORMS_LIBRARY      /home/ibanez/local/lib/fltk_forms.a
FLTK_GL_LIBRARY         /home/ibanez/local/lib/fltk_gl.a
FLTK_IMAGES_LIBRARY     /home/ibanez/local/lib/fltk_images.a
FLTK_INCLUDE_DIR        /home/ibanez/local/include

Note that FLTK on Unix/Linux *MUST* be installed. The reason is that FLTK has an inconsitent convention for the use of upper/lower case in file names and resolved this inconsistency by duplicating *ALL* the headers' filenames with symbolic links. These links are created during the installation process. If you don't install FLTK, you will not be able to find the headers because the case will not match the #includes in ITK.

Find library for a given class

Assume you are using some class in your program and would like to know which library you have to link to your program... Unfortunately there is not a direct way of finding in what library you will find a class. The rule of thumb is that ITK creates a library per each one of the directories in

                        Insight/Code/

and the library name matches the directory name, like ITKCommon, ITKAlgorithms, ITKBasicFilter...

Let the symbol that you are looking for be itk::NumericTraits<float>::One, the itkNumericTraits.cxx file is located in Insight/Code/Common, so you will find the symbol in ITKCommon.lib.

              find . -name "*NumericTraits*"

would have led you to the "Insight/Code/Common" directory, and therefore gave you the hint of using the ITKCommon library.

Platform-specific questions

Build->Rebuild All in MS VC++ reloads all projects

When performing a "Rebuild All" from Microsoft Visual C++, every project prompts the user for a reload (and there are hundreds of projects).

DO NOT USE "Rebuild All" or "Batch Build". Use the following recommended procedure.

There is an ALL_BUILD target available in the MSVC++ workspace. The best way to build ITK is to set ALL_BUILD as the active project, then select the active configuration you want (DEBUG, etc).

This can also be done from the command line like this: msdev ITK.dsw /MAKE "ALL_BUILD - Debug" /REBUILD

Highlighting .txx files in Visual Studio

How can I get Visual Studio to do syntax hightlighting in the files with extension .txx ?

There are four ways to do this:

1. The WRONG way
2. The DANGEROUS way
3. The NICE way
4. The OPEN SOURCE way

The WRONG way

The WRONG is to mark the .txx files as "Compilable". This is WRONG because the .txx files are only intended to be compiled when they are invoked from a .cxx file. Doing this will result in errors such as the ones reported in.

  http://public.kitware.com/pipermail/insight-users/2005-December/015847.html

which after many email exchanges were identified

  http://public.kitware.com/pipermail/insight-users/2005-December/015905.html

The DANGEROUS way

The DANGEROUS way is to make changes in the Windows Registry entries of Visual Studio.

http://public.kitware.com/pipermail/insight-users/2005-November/015785.html

You should avoid doing this since it brings *Bad Karma*. Once you touch the Windows Registry, the consequences will follow you in the afterlife (regardless of whether you believe in the afterlife or not).

The NICE way

This thread for VS8 does not work:

http://public.kitware.com/pipermail/insight-users/2005-November/015786.html

Go the OPEN SOURCE way.

The OPEN SOURCE way

STOP Using the Visual Studio editor, behave as a real programmer and use a decent source code editor such as VIM or EMACS. You can configure these editors to be the default editor used by the Visual Studio IDE.

Borland 5.5 Compiler Issues

To build Insight using the (free) Borland 5.5 compiler:

1. Get the Borland compiler from http://www.borland.com and install it
2. Run cmakesetup and select the Borland Makefiles in the "Build For:" drop down.
3. Set the CMAKE_BUIlD_TYPE to MinSizeRel. This is required so that the Borland linker will stay below its size limit which is arounbd 35 meg for a tds file.

Borland 5.6 Compiler Issues

Well ITK simply does not support this compiler at all.

Windows + FLTK: unresolved external symbol TrackMouseEvent

This error is due to changes in FLTK and it is totally unrelated to ITK. The error only appears in ITK demo applications that are using FLTK for GUI.

The library "comctl32" must be added to the link command line.

You can solve this by editing the CMake file: CMake/Modules/FindFLTK.cmake and around line 39 add the comctl32 library.

After the change the lines should look like:

IF(WIN32)
  SET( FLTK_PLATFORM_DEPENDENT_LIBS wsock32 comctl32 )
ENDIF(WIN32)

This is already fixed in the CVS version of CMake FindFLTK.cmake.

The CMake version 1.6 will have this issue solved.

Mac OS X

Highlighting .txx files in Xcode

Xcode does not recognise the .txx file extension as C++ code, and so one does not see proper syntax highlighting. You can correct this on a per-file basis by choosing Format > Syntax Coloring > C++.

Getting Shared Libraries to work

There is a problem with the Xcode 1.5 tool chain that prevents shared libraries from working. Fortunately, the Mac folks have fixed the problem. You have to update Xcode, the compiler and as much stuff as possible, and it will work again, after you start from a clean build. If gcc -version reports anything less than 3.3 build 1671, then you should update the compiler. From the Apple developers download http://developer.apple.com/macosx/download/ you have to login to get the November2004GCCUpdater.

If you are using Xcode 2.0 or later, there should be no problem.

Under Mac OS X, when I try to run a program that builds successfully, the window is displayed but I can't interact with it.

This is caused by the fact that the application needs to be registered with the window manager for correct operation. There is an additional step that needs to be performed after the link step, in order to add the required resources to the binary. This can be done with a simple:

% /Developer/Tools/Rez Carbon.r -o myapp

For apps built with FLTK, you can use:

% /Developer/Tools/Rez /usr/local/include/FL/mac.r -o myapp

Here is an example of adding a custom command to do this automagically in your `CMakeList.txt` file:

IF(APPLE)
  FIND_PROGRAM(APPLE_REZ Rez /Developer/Tools)
  ADD_CUSTOM_COMMAND(TARGET MyApplication
    POST_BUILD
    COMMAND ${APPLE_REZ}
    ARGS ${FLTK_INCLUDE_DIR}/mac.r -o MyApplication)
ENDIF(APPLE)

Note: This is not required for applications build against X libraries; only for Carbon-based applications. If you have built FLTK for X rather than Carbon, the above does not apply.

(Gavin Baker, 7-May-2004)

How to set Windows DLL's on the Path

In Windows 95 and 98

1. Click on the "Start" button on the task bar.
2. Click on the "Run..." button
3. Type "sysedit". This is the editor of the system files, including the "autoexec.bat"
4. If you have already a PATH variable, then add the directory where the ITK DLLs are to that list. Use ";" as separators
5. If you don't have a PATH variable.... well... add one and put your directory there. It should look like

  PATH=C:\itkbin\bin\Release\

In Windows XP Method A

1. Go to "Control Panel"
2. Select "System",
3. Take the "Advanced" tab
4. Click on the button "Environment Variables" on the bottom,
5. Select "PATH"
6. Add the full directory where you have your ITK .dlls. Pay attention to whether they are in the Release or Debug subdirectories.

In Windows XP Method B

1. Right-Click on "My Computer" ( a popup menu should appear, the last option on it is "properties")
2. Select "properties" a new popup window appears with some tabs on it.
3. Select the tab "Advanced"
4. At the bottom you will se a button called "Environment Variables". Click on it.
5. A new popup window appears with a small browser with the list of environment variables. In this browser you will see the list of environment variables.
6. Select "path" and click on the "edit" button. A small new popup appears with two text fields: "Variable name" and "Variable value".
7. Go to the "Variable value" field, move to the end, add a ";" separator and type the directory where you have the VTK or ITK Dlls.
8. Add another ";" separator and type the directory where you have the ITK Dlls.
9. Click on "OK" to close the "Edit User Variable" window.
10. Click on "Ok" on the "Environment Variables" window.
11. Click on "Ok" on the "System Properties window".
12. Take a deep breath, cross you fingers and try to execute your program again.

Maximum Length for the Windows PATH variable

• Limitation:

 8191 characters (Windows XP)
 2047 characters (Windows 2000 or NT 4.0)

• Solution for a given executable:

 copy the dlls into the executable directory

• General solution:

 Control Panel
  '- System
      '- Advanced
           '- Environment variables
                '- System Properties
                    '- System Variables
                        '- New
 In the popup window:
 Variable name: ITKDebug
 Variable value: c:/cygwin/home/Sylvain/ITKDebug/lib/debug
 Click OK
 Scroll to 'Path' and click 'Edit'
 In Variable value, add at the end of the line (click on the 'End' key): %ITKDebug%
 Repeat this operation for every library path...
 until you reach the maximum path length. ;-)

• Solutions from http://support.microsoft.com/default.aspx?scid=kb;en-us;830473

The limitation applies to the command line, individual environment variables (such as the PATH variable) that are inherited by other processes, and all environment variable expansions. If you use Command Prompt to run batch files, this limitation also applies to batch file processing.

1. Modify programs that require long command lines so that they use a file that contains the parameter information, and then include the name of the file in the command line.
2. Modify programs that use large environment variables so that the environment variables contain less than either 2047 or 8191 characters (as appropriate to your operating system).
   1. Use shorter names for folders and files.
   2. Reduce the depth of folder trees.
   3. Store files in fewer folders so that fewer folders are required in the PATH environment variable.
   4. Investigate possible methods that you can use to reduce the dependency of PATH for locating .dll files.

Visual Studio 6 Compiler Issues

ITK requires service pack 5 or higher to build with Visual Studio 6. However, there are still some code patterns occasionally encountered when using ITK code that cause an INTERNAL COMPILER ERROR. Here is a minimal example of code that reproduces the ICE:

namespace N { template <class T> struct C {}; }
template <class T> struct A
{
  // Inside this template we refer to another template in another namespace.
  void m(const N::C<int>&);
};

// Now declare a class template using a non-type template parameter.
template <unsigned int V> struct B;

The above code results in an ICE reported from line 1794 of msc1.cpp. The work-around is to use a typedef to refer to the other template:

namespace N { template <class T> struct C {}; }
template <class T> struct A
{
  typedef N::C<int> NCint;
  void m(const NCint&);
};
template <unsigned int V> struct B;

Here is another example causing a crash in the same place:

// Create a class template that has type and non-type arguments with defaults.
template <class T=int, int N=1> class A {};

// Require the compiler to deduce the arguments for a specific instantiation.
template <class T, int N> void f(A<T,N>) {}
void g() { f(A<int,1>()); }

The work-around is unforunately to not have the first default template argument:

template <class T, int N=1> class A {};
template <class T, int N> void f(A<T,N>) {}
void g() { f(A<int,1>()); }

There are other code patterns that cause the same error. If you find one please try to produce a minimal example and add it to this page.

Visual Studio 6 Compiler : Why you should not use it

Visual Studio 6 is becoming a really old compiler if you are thinking of using it for your project be ready to bang your head against the wall. Anyway if you have to use it, here are some fixes to the compiler include file (mostly STL related):

• Fixes for Library Bugs in VC++ V5.0/V6.0
• Known problems in using the Microsoft Visual C++ compiler, version 6.0

Visual Studio 7 .NET 2002 Compiler Issues

The Visual Studio 7.0 compiler is more similar to the version 6 compiler than the version 7.1 compiler from the C++ conformance perspective. While it does not crash as frequently as version 6, there are some code patterns that still cause an INTERNAL COMPILER ERROR. Here is one example:

// Define a class template that has a data member of the template type.
template <class T> struct A { T v; };

// Define a primary template with no members.
template <class T> struct B {};

// Define a specialization that defines a type.
// This line is not actually necessary to cause the ICE but will be present when this problem is encountered in practice.
//template <> struct B<int> { typedef int Type; };

template <class T> struct C
{
  // Lookup the "Type" member of B<T>.  In practice this will reference a specialization.
  typedef typename B<T>::Type Type;

  // Use the result of the lookup to instantiate A<> and its data member.
  typedef typename A<Type>::A AType;
};

This will cause an ICE in msc1.cpp, line 2844. The work-around is to define the "Type" member in the primary template of B even though it will not be used:

template <class T> struct A { T v; };
template <class T> struct B { typedef T Type; };
template <class T> struct C
{
  typedef typename B<T>::Type Type;
  typedef typename A<Type>::A AType;
};

Visual Studio 8 .NET 2005 Issues

Deal with Runtime Exceptions in a Managed C++ Windows Forms Application

When such an application uses ITK, it produces runtime exceptions, such as 'System.TypeInitializationException' or memory assertions.

To prevent this, put classes that use ITK into a separate CLR library. Do not make your Forms Application dependent on ITK, but on this library only. You can follow these steps:

1. Create C++ CLR Windows Forms Application,
2. Add to your solution a new Visual C++ CLR Class Library; the benefit of a CLR library is that you don't need to include headers in your Forms Application to use classes from the library, hence your Forms Application may know nothing about ITK
3. Set in this library all ITK directories, include, libraries as you would do so in a not managed application (C/C ++ -> General->Additional Include Directories, Linker->General->Additional Library Directories and Linker->Input->Additional Dependencies); if you have problems, use CMake to generate settings for a not managed application using some sample code and copy these settings
4. Add a reference to this Class Library in your Forms Application
5. In your Class Library, wrap ITK processing into managed classes, you can then use these classes from your Forms Application
6. Remember about linking your Class Library with ITK against matched runtime libraries (C/C++ -> Code Generation -> Runtime Library should match in both your Class Library and ITK project properties)
7. In your Forms Application, you can use VTK to visualize results
   1. VTK can be used in a Forms Application without putting it into a separate class library
   2. you need to change /clr:pure to /clr (Project Configuration Properties->General->Common Language Runtime support) in the Forms Application
   3. your Class Library can export ITK processing results to VTK using itk::VTKImageExport and vtkImageImport (use ConnectPipelines to link these two - the usage and the method's implementaion can be found across ITK sample applications)
   4. if your Class Library uses e.g. vtkImageImport in a public interface, remember about including the directive #pragma make_public(vtkImageImport) in your sources

You should keep in mind that ITK processing in a CLR application is very slow, even when compiled without debug information (using Release configuration). It's best to create even one more library, pure C++ DLL, no CLR, put there the whole ITK processing pipeline and expose only output filters. This way you may have:

1. C++ DLL, no CLR, in which you have defined the whole ITK pipeline
2. C++ library, with CLR (if you need it), that depends on ITK, VTK and the first library. It connects the output of the first library to the input of itk::VTKImageExport, which in turn is connected to vtkImageImport as described above.
3. C++ Windows Forms application CLR, which depends only on VTK and on the second library.

Using the above 3-part configuration instead of CLR-only components, has shortened the processing time in my application from about 10 minutes to 20 seconds(!).

(Tadeusz Dracz, Oct-4-2006)

MipsPro Compilers (7.3.3.1m and 7.4.2m) on IRIX

There have been reports of problems building ITK on IRIX platform. Here are the compiler flags that are used to build ITK and submit nightly dashboard results. SGI Flags for both 7.3.3.1m and 7.4.2m compilers that are working for the kraepelin.uiowa nightly builds.

DEBUG BUILD: //No help, variable specified on the command line. CMAKE_CXX_FLAGS:STRING= -n32 -g -DUDEBUG -G0 -multigot -no_auto_include -xansi -LANG:std -LANG:ansi-for-init-scope=ON -woff 15,84,1110,1209,1424,1468,3102,3210,3439

//No help, variable specified on the command line. CMAKE_C_FLAGS:STRING= -n32 -g -DUDEBUG -G0 -multigot -xansi -woff 15,84,1110,1209,1424,1468,3102,3210,3439

OPTIMIZED BUILD: CMAKE_CXX_FLAGS:STRING= -n32 -O3 -DNDEBUG -G0 -multigot -no_auto_include -xansi -LANG:std -LANG:ansi-for-init-scope=ON -woff 15,84,1110,1209,1424,1468,3102,3210,3439

//No help, variable specified on the command line. CMAKE_C_FLAGS:STRING= -n32 -O3 -DNDEBUG -G0 -multigot -xansi -woff 15,84,1110,1209,1424,1468,3102,3210,3439

Testing

Is ITK tested regularly?

ITK is tested throughout the day on machines distributed around the world. You can view the results at:

http://www.itk.org/Testing/Dashboard/MostRecentResults-Nightly/Dashboard.html

or

http://www.cdash.org/CDash/index.php?project=Insight

ITK uses Dart and CDash to perform builds, run tests and generate dashboards. You can find more information about Dart at http://www.itk.org/Dart/. You can find more information about CDash at http://www.cdash.org.

What is the testing schedule?

Dart opens a daily dashboard at 1:00AM Eastern Daylight Time and keeps that dashbooard open for 24 hours. Build/Test results submitted as "nightlies" will appear on the currently opened dashboard. Each test site can select a convenient time to run tests.

Fresh dashboards are generated every hour, on the hour. They can also be generated on demand using the Rollup button on the dashboard. This button should be used sparingly since dashboard rollups can be time consuming.

In addition to nightly testing, several sites run Continuous build/tests. These sites monitor cvs repository activity and begin a build/test sequence if there are updates to the repository. If a compile error is detected, the Dashboard server sends email to the "offending" party.

What kind of testing is performed?

ITK has three types of tests:

1. Unit Tests. Also called white box tests. These tests reside in the Testing/Code/XXX directories. There are meant to exercise a class's methods and verify that the code compiles, links and produces expected results. These tests do not need to produce results that are useful to a user. If a test returns a 0 status, it passes. A test fails if it returns a non-zero status.
2. Blackbox Tests. These tests are automatically (or semi-automatically) generated. For example, each Code directory has a test called itkXXXHeaderTest. This test is automatically created and has a "#include" for each file in the directory.
3. Regression Tests. These tests generate results and compare them with a known result. The purpose of regression testing is to detect changes in the output of the system.

What is a continuous build and how can I contribute one?

Continuous builds run throughout the day and report their output in the Continuous Builds portion of the dashboard. The most recent build is at the top of the list. The builds run periodically and check the status of the repository. If a file is added or changed since the last build, the working repository of the continuous build is updated, the code compiled and tests executed. Optional e-mail norifications can be sent if there are errors, warmings or test failures.

You can set up a continuous build. This entails writing some small shell scripts and setting up a scheduler (Scheduler for Windows, cron for Linux/Unix). You will also need to install tcl, checkout Dart and configure your build for testing.

For Windows 2000, here are three batch files that can be modified for your own environment.

AllowInsightContinuous.bat
BuildInsightContinuous.bat
PreventInsightContinuous.bat

The batch files use a lock to prevent/allow the continuous

rem ************* AllowInsightContinuous.bat
rem Allow the Continuous to run
rem
c:
cd c:\lorensen\InsightContinuous\Insight-VC6
if EXIST continuous.lock (
  del continuous.lock
)
cd ..
rem ************* BuildInsightContinuous.bat
rem DO a C++ Build Continuously
rem
c:
rem Setup proxy it behind a firewall
set HTTP_PROXY=webcache
set HTTP_PROXY_PORT=8080
rem
rem Setup the path
rem
set PATH=c:/lorensen/InsightContinuous/Insight-VC6/bin/Release;%PATH%
rem
rem Tell cvs where .cvspass resides
set HOME=c:/lorensen
cd c:\lorensen\InsightContinuous\Insight-VC6
if EXIST continuous.lock (
  exit /B
) else (
  date /T > continuous.lock
  time /T >> continuous.lock
  cd c:\lorensen\InsightContinuous\Insight-VC6
 tclsh83 c:/lorensen/Dart/Source/Client/DashboardManager.tcl DartConfiguration.tcl Continuous Start Update Configure Build Test Submit
 cd c:\lorensen\InsightContinuous\Insight-VC6
 del continuous.lock
 cd ..
)
rem ***************** PreventInsightContinuous.bat
rem Prevent the Continuous
rem
c:
cd c:\lorensen\InsightContinuous\Insight-VC6
if EXIST continuous.lock (
  exit /B
) else (
  echo "Prevent continuous for nightly" > continuous.lock
)
cd ..

Now you need to establish a schedule for the three batch jobs. Use the "Scheduled Tasks" on the "Control Panel" to access the Schedule Task Wizard. The following schedule runs the continuous every 10 minutes from 6:05AM until 12:00AM. The Allow and Prevent scripts turn the build ON/OFF at the appropriate time. Schedule each batch file as follows:

AllowInsightContinuous.bat - Daily, Start 6:00AM
BuildInsightContinuous.bat - Daily, Start 6:05AM, Advanced: Repeat Task every 10 minutes, duration 17 hours and 55 minutes
PreventContinuous.bat - Daily, Start 12:00AM

Working with Image Data

How do I iterate through all the pixels in an image?

This requires the use of image iterators, which is explained in detail in the SoftwareGuide in Chapter 11, pdf-page 481.

Examples are available in `Insight/Examples/Iterators`. You probably want to use the ImageSliceIterator.

(Luis Ibanez, 7-Jun-2004)

What are Hounsfield Units?

Hounsfield units were defined by Sir Godfrey N. Hounsfield, on of the pioneers of Computer Tomography for clinical applications.

The units represent the linear attenuation of X-Rays for a particular material.

The units scale is defined in such a way that level for Water is 0 and the level for Air is -1000.

The attenuation of any other material is mapped linearly into this range.

A table of Hounsfield units for common human tissues is avalable in the following link ITK Hounsfield Units

What are MRI T1 / T2 Units?

MRI images measure two types of relaxation times.

The units are millisecons and the two relaxation concepts relate to how long it takes for the molecules in the tissue to realign themselves with a magentic field after being perturbed.

Details on the MRI units are available in the Wikipedia:

Relaxation (NMR)

DICOM: Bits Allocated, Bits Stored and High Bit

A question that is often asked on insight-users is : I am trying to read/write a DICOM image, but some of the DICOM fields have changed after I write it back on disk.

Here is what you have on disk:

        Bits Allocated = 16
        Bits Stored    = 12
        High Bit       = 11

                          |<------------------ pixel ----------------->|
            ______________ ______________ ______________ ______________
           |XXXXXXXXXXXXXX|              |              |              |
           |______________|______________|______________|______________|
            15          12 11           8 7            4 3            0

Here is what you generally get after writing by GDCM:

        Bits Allocated = 16
        Bits Stored    = 16
        High Bit       = 15

            |<------------------------- pixel ------------------------>|
            ______________ ______________ ______________ ______________
           |              |              |              |              |
           |______________|______________|______________|______________|
            15          12 11           8 7            4 3            0

Since DICOM V3, you cannot store any overlay in the unused bits of the Pixel Data (0x7fe0,0x0010), thus it imply that the unused bits are zeros. In ITK, there is no such thing as 12bits Pixel Type, thus when instanciating your reader you declare a 16bits Pixel Type. This buffer is then passed back to GDCM which sees an array of 16bits values and then simply used the simpliest way to store this buffer back on disk: Bits Stored = 16 and High Bit = 15. In case you have not made any change to your pixel buffer, implicitely the first 4 bits will be zero again. The only difference being that they are not as clearly declared as 12bits.

DICOM: Rescale Slope/Intercept

Another question that is often asked on insight-users is : I am trying to read/write a DICOM image, but the pixel data has changed (the scalar range has changed from input file).

This surely comes from the fact that you did not used the proper PixelType to instanciate your reader. You have to consider :

• Bits Allocated
• Bits Stored
• Pixel Representation
• Samples per Pixel

AND:

• Rescale Intercept
• Rescale Slope

For instance you can use the DicomImageReadPrintTags example in ITK/IO

$ DicomImageReadPrintTags image.dcm | grep "Slope\|Intercept\|Bits\|Pixel Rep"
(0028|0100) Bits Allocated = 16
(0028|0101) Bits Stored = 12
(0028|0103) Pixel Representation = 0
(0028|1052) Rescale Intercept = -1000
(0028|1053) Rescale Slope = 1

In this case when you look only at how the pixel are stored on disk: Bits Allocated, Bits Stored and Pixel Representation, you clearly see that they are stored as unsigned short. However looking now at how the pixel are mapped to real world value you need to apply an afine transform:

 RWV = slope * SP + intercept

In which case you'll get signed value. Therefore you will need a signed short pixel to display the pixel value.

One might ask, how can I be sure that signed short will be enough for loading the stored pixel value ? You have two clues: either look at pixel stored: 12bits, therefore you know that signed short will be enough. Or you can have a look sometimes at Smallest Image Pixel Value / Largest Image Pixel Value. It will tell you what are the min/max in your stored image:

$ DicomImageReadPrintTags image.dcm | grep "Image Pixel Value"
(0028|0106) Smallest Image Pixel Value = 0
(0028|0107) Largest Image Pixel Value = 4095

Data Display

What imaging software is available for displaying medical image files?

Here are some viewing options for the image fileformats supported in ITK:

1. Scalar images:

• InsightApplications/ImageViewer
• ParaView
• For 3D images: VolView
• ImageJ

2. Color Images:

• InsightApplications/ColorImageViewer
• ParaView
• For 3D images: VolView

3. Vector Images:

• ParaView (glyphs, streamlines, composites).

When I view the output of my program, all I see is a black image. What went wrong?

ITK is capable of reading and writing data in a variety of formats and bit depths. However many 'consumer' image programs only work with 8-bit data, so when you try to display a 16-bit data file the image will appear black. The solution is to use an image display program that correctly handles these types of files. A small selection is listed above.

ImageMagick is a particularly useful set of tools for image display, manipulation and conversion.

The `ImageViewer` program, part of InsightApplications, is capable of correctly loading and displaying all file types supported by ITK (including anisotropic images).

(Gavin Baker, 24-Jun-2004)

Registration

Can ITK be used for multi-modal registration? For example, CT-MRI, or MRI-fMRI?

ITK provides several method for performing Multi-Modality registration. These methods are described in detail in the SoftwareGuide Chapter 8, pdf-page 241 to 340. In particular you will find interesting Section 8.4 in pdf-page 255 where the Mutual Information metrics are described.

Examples on multimodality registration are available in `Insight/Examples/Registration`. A demo application using Mutual Information is available under `InsightApplications/LandmarkInitializedMutualInformationRegistration`.

It is strongly recommended that you read the chapter on image resampling (Section 6.9.4 of the pdf) before you get involved with image registration methods. That will save you a lot of misunderstandings that are common in new users.

You will also find useful the tutorial sessions, in particular the overview.

(Luis Ibanez, 7-June-2004)

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