= 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.

== 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.

== Software ==
This section explains which volunteers contribute their free time to maintaining and updating the following freeware packages. For all commercial software, please see the committee responsible for purchasing the software.

Manager: the person responsible for making sure that the software is as updated as users of this package require (often this is the most experienced/most vocal user).

Maintainer: the person responsible for performing updates to the software.

Contributors: these persons are the people who offer updates to pieces of the software, but are not in charge of entire releases.
||||||||||<style="text-align: center;">'''Software''' ||
||Package ||<^>First port of Call (i.e. wiki page)||<style="vertical-align: top;">Manager ||<style="vertical-align: top;">Maintainer ||<style="vertical-align: top;">Contributors ||
||EEG Lab ||<^> ||<style="vertical-align: top;">Jason Taylor ||<style="vertical-align: top;">Jason Taylor ||<style="vertical-align: top;">Jason Taylor ||
||<style="vertical-align: top;">Fieldtrip ||<^> ||<style="vertical-align: top;">Jonathan Peelle ||<style="vertical-align: top;">Jonathan Peelle ||<style="vertical-align: top;"> ||
||Freesurfer ||<^> ||<style="vertical-align: top;">Daniel Wakeman ||<style="vertical-align: top;">Daniel Wakeman ||<style="vertical-align: top;">Daniel Wakeman ||
||FSL ||<^> ||<style="vertical-align: top;">??? ||<style="vertical-align: top;">??? ||<style="vertical-align: top;">??? ||
||<style="vertical-align: top;">MNE ||<^> ||<style="vertical-align: top;">Daniel Wakeman ||<style="vertical-align: top;">Daniel Wakeman ||<style="vertical-align: top;">Daniel Wakeman ||
||<style="vertical-align: top;">SPM ||<^> ||<style="vertical-align: top;">Rhodri Cusack ||<style="vertical-align: top;">Rhodri Cusack ||<style="vertical-align: top;">Daniel Mitchell, Jason Taylor, Rik Henson, Rhodri Cusack ||