The Computational Morphometry Toolkit
==========================================================================
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 32bit (Fedora 17), gcc 4.7.0
- Linux 64bit (Fedora 17), gcc 4.6.3, 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 4.7.1, 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/
==========================================================================
Changes:
Release CMTK-2.2.3 (2012-08-10):
(r4475) Added: new "contrib" directory for third-party contributions;
initially Greg Jefferis' "munger" Perl script.
(r4470) Added: new "groupwise_reformat" script simplifies reformatting all
images in a set aligned with one of the groupwise registration
tools.
(r4458) Fixed: older versions of FFTW than 3.3.2 now supported again.
(r4456) Fixed: when reading NRRD files with missing "spaceOrigin" entry,
CMTK now substitutes a zero-vector for the origin, rather than
keeping NrrdIO's not-a-number values.
(r4454) Fixed: the index-to-physical matrix of a UniformVolume was not
properly modified when downsampling with pixel selection (rather than
averaging).
(r4449) Added: when installed system mxml library is found, its version is
determined, and the bundled library is automatically built if the
system library is outdated (pre-2.7).
(r4447) Added: new tool, "dwi_find_bad_slices," to detect bad slices in
sets of diffusion-weighted images.
(r4447) Changed: image-to-physical matrix and slice spacing now work
properly (as in, without generating Inf/NaN values) when splitting
volume into single slices and re-stacking it. This has caused some
baselines to change, because the volume field of view sizes have
seen subtle changes as a result.
