AnalysisSoftware - MRC CBU Imaging Wiki

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Revision 26 as of 2009-10-16 15:00:40

location: AnalysisSoftware

Software

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

General computing

Programming

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