Keep up to date with this [:ImagingComputingDevelopments:list of latest software developments]

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. 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] - 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

Other tools you might find useful

• [wiki:UsingVNC Using VNC at the CBU] - gives you a graphical desktop on the linux machines from your desk

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