software


 

mat1dump [.pl]

A perl script to dump the contents of a Matlab (version 4.x) file to ASCII text.
This was written from the Matlab file format, now accesible from www.mathworks.com/..../matfile_format
It most likely has limited functionality as I only wrote it to read in SPM header files.
If you are interested in this, you'll also be interested in matdump to dump Matlab 5.x files.

ana2mnc

A perl script intended to be the swiss army chainsaw of MINC <-> SPM <-> ANALYZE 7.5, currently there is support for all the fields (that I know of) of the ANALYZE 7.5 header and MINC support is also fully functional. There are plans afoot to support the SPM .mat "normalization" files during the conversion to preserve orientation and scaling.
ana2mnc can be called in 4 different ways (via links)
ana2mnc - convert an ANALYZE 7.5 file (.hdr .img pair) to a MINC file
mnc2ana - convert a MINC file to an ANALYZE 7.5 file (.hdr .img pair)
ana_show - Show the contents of an ANALYZE 7.5 header
ana_write - write an ANALYZE header (requires gobs of additional CL arguments)
MINC is a free file format based upon netcdf from the MNI
ANALYZE is a commercial file format from the mayo clinic
SPM is a free fMRI toolkit from the FIL using a hybrid ANALYZE format
NB the use of this is now deprecated in favor of nii2mnc that is now part of the base MINC install
See http://packages.bic.mni.mcgill.ca/tgz  for MINC

unc2mnc [.tar.gz]

A perl script to convert, dump header contents and view (via MINC conversion) UNC files to MINC format. I have no immediate plans to offer ANY conversion to UNC, however if you are interested in this, it would not be all that hard to achieve
unc2mnc can be called in 3 different ways (via links)
unc2mnc - convert a UNC file to a MINC file
uncdump - dump the header portion of a UNC file
uncview - view a UNC file via conversion to MINC
MINC is a free file format based upon netcdf from the MNI
UNC is a vaugely ANALYZE'ish format used by some. (Notably the BAMM software of UCL)

mincblob

mincblob is used to compute the trace (volume increase or decrease - dilation) or translation (local volume changes that relate to movement of tissue not related to dilation) of a vector deformation field as produced by ANIMAL non-linear registration.
For more information on the maths behind this: a paper
See http://packages.bic.mni.mcgill.ca/tgz  to download the latest version

mincfbbox [.tar.gz]

A slight modification of the mincbbox program found in the ANIMAL package.
A -frequency option is introduced, allowing you to specify a number of over-threshold voxel before a boundary is detected. I found this method a little more robust on noisy data.

mincgroup [now-part-of-mincmorph]

mincgroup counts both the size and number of "groups" of voxels within a file.
See http://packages.bic.mni.mcgill.ca/tgz for mincmorph 

mincpik [now-part-of-minc-core]

Generates image files (.jpg .png .tiff etc) from MINC files with respect to step sizes.
See http://packages.bic.mni.mcgill.ca/tgz 

mincstats [now-part-of-minc-core]

Calculates histograms and statistics of minc files. (a stand alone mutation of volume_stats and volume_hist in the N3 package)
See http://packages.bic.mni.mcgill.ca/tgz 

minctiller [.tar.gz]

A MINC version of tiller

pv2mnc [.pl]

A perl script to convert a specific Bruker Paravision expno-procno to MINC format.
this script is mainly kept here for historical reasons. Mathew Brett has written a far more complete paravision converter that now has MINC support called pvconv.
http://pvconv.sourceforge.net/