Release Name: 2.3.0
Notes:
The Computational Morphometry Toolkit
==========================================================================
Release Notes -- CMTK 2.3.0
===========================
This release of CMTK incorporates some major bug fixes and improvements. Most
notable the ADNI phantom detection tool can now robustly handle a variety of
real-world problems, such as broken phantoms.
The "dcm2image" tool no longer puts potentially protected information, such as
device identifiers or dates, into XML sidecar files.
This release also bundles the complete SRI24 atlas with all template images
and a variety of labels maps for volumetry and DTI fiber tracking.
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
- Windows 7 64bit, VisualStudio 2012 Express for Desktop, 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/
==========================================================================
Changes:
Release CMTK-2.3.0 (2013-05-16):
(r4751) Added: ADNI phantom detection tool now also functions when the
60mm SNR sphere is displaced.
(r4732) Added: ADNI phantom detection tool can now robustly bootstrap gross
orientation from CNR spheres if one or both of the 15mm phantom
spheres are missing.
(r4719) Added: dilation and erosion in anisotropic images by distance, not by
pixels.
(r4708) Added: ADNI phantom detection is now more robust in the presence
of missing, cropped, or low-contrast marker spheres.
(r4703) Added/Changed: dcm2image now only exports potentially protected,
identifying meta-data (e.g., UIDs, paths, dates) into XML files if
specifically instructed to do so.
(r4699) Added: ADNI phantom detection tool now recognizes when marker spheres
are (partially) outside image field of view. Optional "tolerant" mode
can override program termination.
(r4690) Added: ADNI phantom description file (XML) now contains estimated
scale factors and nonlinearity.
(r4684) Added: pixel search tool, "pxsearch." For now, this simply
searches for the pixel with the maximum value in a local
neighborhood.
(r4680) Fixed: use of stat() rather than stat64() broke access to files on
large file systems.
(r4674) Fixed: FFTW dependency was not really options due to incorrect
configuration conditions (Issue #6841).
(r4670) Fixed: an error in WarpXform::ReplaceInitialAffine broke
convert_warp tool, specifically the computation of a fractional
transformation. New test cases have also been added to cover this.
(r4662) Fixed: check whether FFTW libraries were found rather than relying on
CMTK_USE_FFTW option being set.
(r4654) Added: N-CANDA script for creating GRE field maps using FSL/prelude
(r4652) Fixed: OpenMP problems using VisualStudio
(r4648) Fixed: configuration problem with CMake 2.8.10 due to changed path to
CMakeSystem.cmake file.
(r4622) Added: N-CANDA structural pipeline in "contrib/ncanda/"
(r4595) Added: more channels of the SRI24 atlas added to the CMTK
repository. The atlas is also now installed and packaged with the
toolkit.
(r4586) Added: Otsu thresholding now integrated into "mrbias" tool.
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