Computational Morphometry Toolkit (CMTK) News

Maintenance release CMTK 3.3.1p1, source code only

Torsten Rohlfing — Fri, 25 Jan 2019 12:36:21 GMT

I am releasing CMTK 3.3.1p1 as source code only, because the only change here is to fix compilation errors resulting from an API change in the DCMTK library (release 3.6.4 thereof, to be precise). There are no other changes, and stable Linux distros are still deploying the older version of DCMTK.

CMTK 3.3.0 Released

Torsten Rohlfing — Fri, 22 Jan 2016 1:47:56 GMT

A new version of CMTK, 3.3.0, is now available for download.

This version fixes a few minor bugs, but mostly lifts a size limit previously imposed on images, which could not contain more than 2 billion pixels. On 64bit platforms, this limit has been removed for most algorithms. Exceptions are inverse interpolation for volume reconstruction and EPI unwarping, both of which are constrained by the use of 32bit vector indexing in the underlying third-party numerical code.

Precompiled binaries are available for Linux, Cygwin, and Windows (all 64bit). If anyone would like to volunteer to contribute binaries for MacOS, please let me know.

CMTK 3.2.3 released

Torsten Rohlfing — Mon, 02 Feb 2015 5:05:23 GMT

A minor bugfix release, CMTK 3.2.3 fixes issues with import of non-integer DICOM data, directory creation on Windows, and a broken release of MXML. This release also integrates a downstream patch from NeuroDebian for fixing bashisms in shell scripts.

Note that unlike previous releases, there will be no Mac builds provided, as I no longer have access to a suitable system. Packaging on Windows 7 (Visual Studio 2013) seems to be broken but may be fixed eventually. A Cygwin build is forthcoming. (Volunteers for providing Mac and native Windows builds would certainly be welcome!)

See CHANGELOG and README.txt files for details on changes and detailed notes about this release.

CMTK 3.2.2 Released

Torsten Rohlfing — Mon, 04 Aug 2014 4:36:08 GMT

We are pleased to announce the release of CMTK 3.2.2.

This release fixes a handful of small but significant bugs (in vtkxform and the transformation concatenation library code). See CHANGELOG for full details.

Sadly, this will be the last release of CMTK coming out of SRI. Future releases will be supported by myself personally but will have no institutional backing. As an immediate side effect, I will no longer be able to provide binary packages for the Windows and MacOS platforms after this release. Volunteers with access to suitable build systems are welcome to come forward at this time.

To be clear - CMTK is not orphaned, but development resources will be somewhat reduced going forward.

Best,
Torsten

CMTK 3.2.0

Torsten Rohlfing — Wed, 07 May 2014 3:38:25 GMT

We are pleased to announce the release of CMTK 3.2.0.

This version brings a number of improvements, such as the ability to extract slice timing information (e.g., for rs-fMRI) and the sign of phase encode direction from Siemens DICOM files and properly fill the respective header fields in NIfTI files as well as write this information to XML sidecar files.

Interoperability with FSL has been improved by allowing the creation (via "xform2dfield") of deformation fields in NIfTI (rather than Nrrd) format, with coordinates adjusted such that the deformation field will properly map coordinates when used with FSL's "applywarp" tool.

Note the following changes to pre-compiled distributions:

- The Linux RPM file has been split into two parts, "core" and "devel", where the former contains everything necessary to use CMTK tools, and the latter contains files only needed for development (e.g., static libraries and header files).

- Going forward, Windows binaries will be generated on Windows 7 (rather than XP) using VisualStudio Express 2012 (rather than 2011).

- For the time being, only ZIP archives will be made available for Windows, since CPack and NSIS are stubbornly refusing to work together on our build system.

Enjoy!

CMTK 3.1.0 released

Torsten Rohlfing — Mon, 03 Mar 2014 1:52:16 GMT

We are pleased to annouce the release of CMTK 3.1.0. This release adds a few new features, such as a polynomial transformation model and support for extracting diffusion imaging metadata from Philips DICOM files. For a detailed list of changes, see the release notes and/or the change log.

This release hopefully also fixes some issues with bad external library dependencies of the Mac OS builds provided through NITRC.

CMTK 3.0 released

Torsten Rohlfing — Fri, 10 Jan 2014 4:18:47 GMT

We are pleased to announce Release 3.0 of CMTK, the Computational Morphometry Toolkit (code name "Cambridge").

This release fixes a number of major problems in earlier releases, specifically:

1. The handling of affine transformation matrices was broken, leading to incorrect derivation of transformation parameters from matrices. CMTK 3 continues to read existing transformation files exactly as earlier versions, but files created by CMTK 3 and later will be different.

2. The handling of image-to-space transformations in NIFTI files (qform and sform) was inconsistent with the NIFTI standard. CMTK 3 will continue to read existing NIFTI files in exactly the same way as earlier versions, but newly created files will differ.

See Release Notes for further details on changed behaviour.

CMTK 2.3.0 released

Torsten Rohlfing — Fri, 17 May 2013 1:28:23 GMT

We are pleased to announce the release of CMTK 2.3.0, which brings a number of bug fixes as well as a vastly improved tool for detection and quantification of the ADNI imaging phantom. This will work even in many cases when the phantom itself is defective.

CMTK distributions now also include the SRI24 atlas for use with some bundled image analysis pipelines.

See Release Notes and ChangeLog for full details.

CMTK 2.2 release adds new features

Torsten Rohlfing — Tue, 08 May 2012 11:28:19 GMT

We are pleased to announce the release of CMTK 2.2 with some exciting new features. Source code and pre-compiled packages are available from CMTK's "Downloads" section on NITRC.

Most importantly, CMTK now has two tools to perform structural MRI unwarping using reference scans of the "ADNI Phantom." The workflow is described in a brief paper over at the InsightJournal:

http://hdl.handle.net/10380/3354

This article can also be downloaded from the CMTK/Docs section on NITRC.

Many other detail fixes and improvements have also gone into this release - check out the ChangeLog for details.

As always, all of CMTK is free as in beer and speech, and you don't even have to make us authors on any of your papers just for using it. Imagine that! (Please do mention CMTK in your Acknowledgments if you use it, though.)

[Note: the original 2.2.0 release had a packaging bug and was replaced with release 2.2.1]

CMTK 2.1.3 minor release

Torsten Rohlfing — Fri, 09 Mar 2012 12:57:41 GMT

We have released CMTK 2.1.3. This release is intended to lock in minor changes and reorganization of the Shape-Based Averaging (SBA) tools and library code, formerly contained in the "average_edt" tool.

Users of CMTK 2.1.2 who are not interested specifically in SBA probably have no reason to upgrade.

Of interest for users on the Mac platform may be the addition of pre-built packages compiled using the MacPorts gcc 4.6 compiler. These builds, indicated by an additional "mp" in the package file name, replace SMP parallelism using GCD with OpenMP parallelism. On dedicated computation servers, this should give substantially improved performance of some CMTK tools, because only a small fraction of algorithms is implemented using GCD support.