
The Computational Morphometry Toolkit
==========================================================================


Release Notes -- CMTK 2.2.6
===========================

This is primarily a bug fix release to address a segmentation fault in the
dcm2image tool, introduced in the previous release 2.2.5.


Release Notes -- CMTK 2.2.5
===========================

The DICOM stacker, dcm2image, has seen a number of recent improvements that
are included in this release.


Release Notes -- CMTK 2.2.4
===========================

This release fixes two problems: a) the echo planar image unwarping tool,
epiunwarp, failed when there were all-zero columns in the input image, and b)
some PACS-processed Siemens mosaic DICOM files were not detected and handled
correctly, due to missing DICOM tags.


Release Notes -- CMTK 2.2.3
===========================

This maintenance release adds a new script for easy reformatting of all images
in a groupwise-aligned set, as well as a registration-and-reformatting script
("munger") contributed by Greg Jefferis (this requires Perl).

In the official "standard" MacOS builds, FFTW is now disabled, as all CMTK
tools would otherwise require MacPorts to be installed. Qt and CUDA support
remain enabled, as these should not interefere with tools that do not use
these libraries. The MacPorts build continues to come with FFTW support
enabled.


Release Notes -- CMTK 2.2.2
===========================

This release adds more transformation fitting tools and completes support for
computing SNR and CNR from images of the ADNI phantom. 

A new tool, "streamxform" will ultimately replace the rather poorly-designed
"gregxform" tool and its confusing and inefficient interface.


Release Notes -- CMTK 2.2.1
===========================

This is a service release that fixes a single bug - CMTK 2.2.0 installed (and
packaged) the entire source code tree, rather than just the Licenses/
directory as intended. This problem has been fixed.


Release Notes -- CMTK 2.2.0
===========================

This release adds significant new functionality to CMTK. The library now
supports fitting transformations (linear and B-spline) to landmark sets. This
is used to support image unwarping based on structural phantom scans. In
particular, CMTK now supports detection (via "detect_adni_phantom") and use
(via "unwarp_image_phantom") of the Magphan(R) EMR051 Quantitative imaging
Phantom (a.k.a. "ADNI Phantom").

Numerous new classes have also been added to the CMTK libraries in the process,
such as a fast FFT-based NCC sphere finding filter, Otsu thresholding, and
regression-based polynomial bias field estimation.

Also new in CMTK are two tools, "fibxform" and "fib2image", to spatially
transform and visualize, respectively, DTI fiber tracts stored in .fib
produced by the UNC Fiber Tracker.

CMTK now requires at least CMake 2.8.0 to build. For FFT-based functions
(including phantom landmark detection) CMTK must be build with FFTW support
(new option CMTK_USE_FFTW).

For a complete list of changes, fixes, and additions, consult the CHANGELOG
file.

CMTK has been built and tested on the following platforms:

- Linux 64bit (Fedora 17), gcc 4.7.2, CUDA 3.2
- Linux, i386, Oracle Solaris Studio 12.3 C++ 5.12 2011/11/16
- MacOSX 10.6, x86_64, gcc 4.2.1, CUDA 4.1
- MacOSX 10.6, x86_64, MacPorts gcc 4.7.2, CUDA 4.1
- MacOSX 10.6, x86_64, llvm-gcc-4.2.1
- MacOSX 10.6, x86_64, clang 2.0
- Cygwin, gcc 4.5.3
- Windows XP, VisualStudio 10SP1 (2010 Express Edition), CUDA 4.1


Platform-Specific Issues
========================


MacOS-X
-------

- Code coverage tests are only supported with gcc compiler and SDK 10.6. Older
  SDKs or the clang and llvm compiler front-ends do not support code coverage.

  http://www.nitrc.org/tracker/index.php?func=detail&aid=5450&group_id=212&atid=877


- To use a pre-compiled binary distribution of CMTK on MacOS, the following
  MacPorts packages have to be installed under /opt/local:
  - qt4
  - sqlite3
  - dcmtk


SolarisStudio Compiler, Linux/Intel
-----------------------------------

- SolarisStudio C++ 12.2 crashes when compiling the "Numerics" library with
  full optimization, -O3. A bug report has been filed with, and accepted by,
  Oracle:

  http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6989625

  Workaround: build "MinSizeRel" configuration, which sets optimization level
    to O2. Note that OpenMP must be disabled, because otherwise optimization
    is bumped back to O3 by default.

  This problem is also fixed in SolarisStudio 12.3, but see next issue.


- SolarisStudio C++ 12.3 crashes when compiling the file
  "cmtkEchoPlanarUnwarpFunctional.cxx" with OpenMP support turned on.

  Workaround: set "CMTK_USE_OPENMP" configuration option to "OFF"; this will
    lead to much of CMTK's functionality executing single-threaded.


Open64 Compiler
---------------

- CMTK does not build in Release mode with the Open64 compiler due to internal
  compiler errors.


==========================================================================

This software is available from

  http://www.nitrc.org/projects/cmtk/

==========================================================================
