= Neuroimaging software =
You might want to [:ScientificComputing:read this overview of scientific computing] and keep up to date with this [:ImagingComputingDevelopments:list of latest developments]

Try the [:StudentForum:student forum for helpful tips]

== Major neuroimaging software packages installed at the CBU ==

Most imagers at the CBU use [:SpmInformation:SPM, the dominant software analysis package from the FIL in London], which runs under [:LearningMatlab:a language called Matlab]. However, [:FslInformation:FSL] ("fossil") - a powerful and fast collection of tools from FMRIB, Oxford, also has a following.

For some applications (particularly flat mapping, or performing grey & white matter segmentation for MEG analysis) you might wish to use [:FreeSurferAnalysis:Freesurfer].

[:AfniInformation:Afni] is also installed.

There is [:AvailableSoftware:a list of the people responsible for maintaining our neuroimaging (fMRI & MEG) software].

== Smaller tools ==
[:MriCro:MriCro and its successor MriCron] are a pair of very useful tools for viewing structural or functional images, producing 3D renderings of activation, and examining anatomical templates.

== Extensions to SPM/Matlab ==
 * [:AutomaticAnalysisIntroduction:aa - automatic analysis] - a system to automate SPM analyses, allowing the easy application of a set of pre-defined analysis recipes
 * MarsBar - a useful toolbox for performing region-of-interest (ROI) analyses
 * [:DataDiagnostics:tsdiffana] - data diagnostics utility, good for checking the quality of your fMRI data
 * SnpmInformation - for doing non-parametric statistics in SPM
 * LoadShare - our tool for balancing SPM jobs across machines
 * SpmBatchPrintContrasts - for printing contrasts automatically
 * DisplaySlices program for displaying multiple images slices in SPM

== Beyond fMRI ==
 * AnalyzingDiffusion
 * UsingFreesurfer

= General software =
== Programming ==
 * LearningUnix
 * LearningMatlab
 * LearningPython
 * ImageDataFormats

== Other tools you might find useful ==
 * [:UsingVNC Using VNC at the CBU] - gives you a graphical desktop on the linux machines from your desk
 * [:CbuSoftware:An archive of other software that you might find useful]

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