MINC/SoftwareDevelopment/EZMINC/MincifiedTools

3rd party tools which were made to understand MINC using EZMINC

Advanced Normalization Tools (ANTS)

Non-linear diffeomorphic registration tool, home page: http://picsl.upenn.edu/ANTS/ MINCIFIED version based on version 1.9 can read .mnc files, if the output have extension is .xfm, it will produce MINC style xfm files for forward and backward transformations. Note that non-linear part is stored in a separate file with suffix _grid_0.mnc (referenced from xfm files)

• Source code: http://www.bic.mni.mcgill.ca/~vfonov/software/mincANTS_1p9_p1.tar.gz

ITK SNAP

Visual tools for manual segmentation of anatomical images, home page: http://www.itksnap.org MINCIFIED version based on version 2.0.0:

• Source code: http://www.bic.mni.mcgill.ca/~vfonov/software/itksnap-2.0.0-minc-src2.tar.gz
• 32-bit Debian package (self-contained does not require minc/netcdf/hdf): http://www.bic.mni.mcgill.ca/~vfonov/software/itksnap-2.0.0-20091117-Linux-i686-fixed-minc.deb
• 64-bit Debian package (self-contained does not require minc/netcdf/hdf): http://www.bic.mni.mcgill.ca/~vfonov/software/itksnap-2.0.0-20091117-Linux-x86_64-fixed-minc.deb
• 32-bit Mac OS X package (self-contained does not require minc/netcdf/hdf) : http://www.bic.mni.mcgill.ca/~vfonov/software/itksnap-2.0.0-20091117-Darwin-i386-fixed-minc.dmg

WARNING: Please upgrade to the latest version of binary package or compile EZminc version r73 or later if using source. A bug was fixed in the previous version leading to occasional corruption of minc files with labels due to inter-slice normalization.

MINCIFIED version based on version 2.2.0:

• Source code: http://www.bic.mni.mcgill.ca/~vfonov/software/itksnap-2.2.0-with-minc.tar.bz2
• 64-bit Ubuntu 11.04 package (self-contained does not require minc/netcdf/hdf): http://www.bic.mni.mcgill.ca/~vfonov/software/itksnap-2.2.0-20110504-Linux-x86_64.deb

NOTE: Due to the differences between neurological and radiological notations mincified version will not correctly display nii files (left-right swap).

ElastiX

Non-linear registration tool, home page: http://elastix.isi.uu.nl/

• Example Mincified Source Code: http://www.cim.mcgill.ca/~dante/code/elastix-4.3_minc.tar.gz

NOTE: Elastix v4.3 has a must be compiled with ITK 3.14. Furthermore, ITK 3.14 must itself be compiled with the CMake variable ITK USE REVIEW set to ON and ITK USE REVIEW STATISTICS also set to ON. Please refer to the manual for detailed building instructions.