Computational Morphometry Toolkit (CMTK)
The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model).
CMTK is implemented in C++ with parallel processing using POSIX Threads (SMP), OpenMP (SMP), Grand Central Dispatch (SMP), and CUDA (GPU).
Supported file formats include Analyze (r/w), NIFTI (r/w), Nrrd (r/w), DICOM (read), BioRad (read). Data exchange with other toolkits, such as ITK, FSL, AFNI, SPM, etc. is thus easily accomplished.
INIA19 Primate Brain Atlas
NCANDA: Data Integration Component
Lightweight Data Pipeline
Recent Activity - Documents
Recent Activity - Trackers
Linux tar distribution requires installation in /usr/local posted by Torsten Rohlfing on Apr 30, 2014
Shear and anisotropic scales not correctly recovered from affine matrix posted by Torsten Rohlfing on Nov 27, 2013
Presence/absence of FFTW threads lib is not tested posted by Torsten Rohlfing on Mar 11, 2013
Image position not correctly read from Siemens mosaic DICOM files posted by Torsten Rohlfing on Oct 2, 2012
image origin and axes directions not set from multi-slice DICOM files posted by Torsten Rohlfing on Aug 24, 2012
Recent Activity - Forums
Issue installing CMTK Gui in Fiji - Mac (Catalina) posted by Greg Jefferis on Oct 9
Issue installing CMTK Gui in Fiji - Mac (Catalina) posted by caroline kibat on Oct 9
Recent Activity - News
Maintenance release CMTK 3.3.1p1, source code only posted by Torsten Rohlfing on Jan 25, 2019