= Software for imaging at the CBU =
== Software ==

Scientific software is managed by members of the imaging community (see below) and by members of the computing group. For queries concerning specific software packages, the people listed below are the best contact in the first instance.

General requests can be sent to members of the Methods group, including [[mailto:olaf.hauk@mrc-cbu.cam.ac.uk|Olaf Hauk]] and [[mailto:tibor.auer@mrc-cbu.cam.ac.uk|Tibor Auer]].

General IT requests should be sent to [[mailto:it-help@mrc-cbu.cma.ac.uk|IT help]]. They will reach the whole IT team, who will decide what to do with them.

The following scientists volunteered to support particular scientific software packages. They can be contacted about computing-related problems, e.g. with respect to updates, missing libraries/toolboxes etc. (note: this does not include analysis support).
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||||||||||<style="TEXT-ALIGN:center">'''Software at the CBU''' ||
||'''Package ''' ||<style="VERTICAL-ALIGN:top">'''Link ''' ||<style="VERTICAL-ALIGN:top">'''Contact ''' ||<style="VERTICAL-ALIGN:top">'''Versions ''' ||<style="VERTICAL-ALIGN:top">'''Comments ''' ||
||EEG Lab ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Jason Taylor, Tristan Bekinschtein ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Fieldtrip ||<style="VERTICAL-ALIGN:top">FieldtripInformation and FieldtripAnalysis ||<style="VERTICAL-ALIGN:top">Maarten van Casteren, Lucy !MacGregor, Olaf Hauk ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Freesurfer ||<style="VERTICAL-ALIGN:top">FreeSurferAnalysis ||<style="VERTICAL-ALIGN:top">Kristjan Kalm, Marta Correia, Olaf Hauk, Tibor Auer ||<style="VERTICAL-ALIGN:top">4.0.1/4.3.0/5.1.0 (glx only) ||<style="VERTICAL-ALIGN:top"> ||
||FSL ||<style="VERTICAL-ALIGN:top">FslInformation ||<style="VERTICAL-ALIGN:top">Marta Correia ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Camino ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Marta Correia ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Real Time MRI ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Marta Correia, Daniel Mitchell ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||MNE ||<style="VERTICAL-ALIGN:top">[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_overview|MNE]] ||<style="VERTICAL-ALIGN:top">Olaf Hauk ||<style="VERTICAL-ALIGN:top">2.5/2.6/2.7.1, MNE_Python ||<style="VERTICAL-ALIGN:top"> ||
||SPM ||SpmInformation (FMRI) CbuMeg:SpmAnalysis (MEG/EEG) ||<style="VERTICAL-ALIGN:top">Rik Henson ||<style="VERTICAL-ALIGN:top">8/5/2 ||<style="VERTICAL-ALIGN:top">Default latest version of SPM8 is FIL official release r4667. There is also a devel SVN version available with local changes. Older versions of SPM5 and SPM2 available. ||
||AA ||<style="VERTICAL-ALIGN:top">[[AA]] ||<style="VERTICAL-ALIGN:top">Daniel Mitchell, Tibor Auer ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Elekta Neuromag ||<style="VERTICAL-ALIGN:top">CbuMeg:NeuromagSoftware ||<style="VERTICAL-ALIGN:top">Yury Shtyrov ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Matlab ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">IT, Russell Thompson ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||R ||<style="VERTICAL-ALIGN:top">http://www.r-project.org/ ||<style="VERTICAL-ALIGN:top">Dennis Norris ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Python ||<style="VERTICAL-ALIGN:top">http://www.python.org/||<style="VERTICAL-ALIGN:top">Dennis Norris ||<style="VERTICAL-ALIGN:top">2.71 ||<style="VERTICAL-ALIGN:top">make sure /imaging/local/software/python64/bin is on your path ||
||C++ ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Maarten van Casteren, Dennis Norris ||<style="VERTICAL-ALIGN:top">4.1.2 ||<style="VERTICAL-ALIGN:top"> ||
||E-Prime ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Maarten van Casteren ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Presentation ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||SPSS ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Peter Watson ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||




== Matlab ==
See our [[http://imaging.mrc-cbu.cam.ac.uk/meg/Beginners|Beginner's pages]] for tutorials etc., or 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.

== Imaging analysis packages ==
 * SPM: see SpmInformation for general information on SPM, and SpmVersions for instructions on running SPM at the CBU.
 * FSL: see FslInformation
 * AFNI: see AfniInformation
 * BrainVisa / Anatomist: see BrainVisaInformation
 * Freesurfer: FreesurferInformation
 * MRIcro: see MriCro

== SPM toolboxes ==
 * MarsBar
 * SnpmInformation

== Other imaging software ==
 * [[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 [[MriCro|MRIcro]] - start with `startmricro` on the Linux machines.
 * 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
 * ImageViewer - a simple matlab image viewer - now very old
 * [[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 [[FormatBruker|Bruker data format]] to [[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 [[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.