Software for imaging at the CBU

Matlab

See LearningMatlab for how to learn and use matlab.

Matlab runs on all the unit imaging Linux machines as well as our Solaris machine, navi (see CbuComputingResources).

Linux machines l02-l07 run Matlab 6; machines l08-l13 Matlab 7.

SPM

See SpmInformation for general information on SPM, and SpmVersions for instructions on running SPM at the CBU.

Other imaging software

• [wiki:UsingAnalyze AnalyzeAVW] - a comprehensive commercial program for viewing neuroimaging data. Particularly useful for rendering. At the CBU, it will only run on the Solaris machines, if atall. Please contact MatthewBrett if you need this program.

• Chris Rorden's [wiki:MriCro MRIcro] - start with startmricro on the Linux machines.

• AFNI - see AfniInformation

• Krish Singh's [http://www.psychology.nottingham.ac.uk/staff/cr1/mri3dtut.html mri3d] - an excellent display tool, particularly for rendering of results onto brain surfaces.

• [http://www.psychology.nottingham.ac.uk/staff/cr1/dicom.html freeware DICOM viewer and information], again for Windows, again by Chris Rorden

• [wiki:ImageViewer Viewer] - a simple matlab image viewer - now very old

• [wiki:Ana4Dto3D ana4dto3d] - a tiny command line utility to convert Analyze 4D files to a series of 3D files, as well as byte swapping as required

• [http://pvconv.sourceforge.net pvconv] - a perl command line utility to convert [wiki:FormatBruker Bruker data format] to [wiki:FormatAnalyze Analyze image format]

• [http://www.fmrib.ox.ac.uk/fsl FSL] - the Oxford FMRIB software library for analyzing functional MRI and diffusion images.

• See also [wiki:ReadingOnlineDocs Software and help on reading documents online] - such as Adobe Acrobat for pdf files and Ghostview for reading postcript (.ps) files.

Other general interest software available on the unit Linux machines

• gimp - Graphics viewing and editing program; the Linux version of Photoshop
• acrobat - PDF viewer.
• mozilla - web browser
• nedit, emacs - text editors
• kghostview - ps / psf / eps viewer useful for SPM postscript files

Many other packages are available from the menu in the bottom right of the windowing environments.