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Most imagers at the CBU use [:SpmInformation:SPM, the dominant software analysis package from the FIL in London], which has consistently been on the cutting edge of new methods. It runs under [:LearningMatlab:a language called Matlab] allowing you to browse the source and write your own components relatively easily. Most imagers at the CBU use [:SpmInformation:SPM, the predominant software analysis package from the FIL in London], which has consistently been on the cutting edge of new methods. It runs under [:LearningMatlab:a language called Matlab] allowing you to browse the source and write your own components relatively easily.
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Neuroimaging software

You might want to [:ScientificComputing:read this overview of scientific computing].

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 predominant software analysis package from the FIL in London], which has consistently been on the cutting edge of new methods. It runs under [:LearningMatlab:a language called Matlab] allowing you to browse the source and write your own components relatively easily.

[:FslInformation:FSL] ("fossil") - a powerful and fast collection of open source tools from FMRIB, Oxford also has many strengths and has a substantial following.

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

[:AfniInformation:Afni] is also installed.

There are some old licenses for Brain Voyager around. This point-and-click commercial package has many impressive features.

It seems we might have [:BrainVisaInformation:Brain Visa] installed but I think it is probably an old version. If you find out, please put the latest information here!

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

Automatic analysis (aa)

A system to automate SPM analyses, allowing the easy application of a set of pre-defined analysis recipes

For version 3.0 and later - the [http://www.cambridgeneuroimaging.com/aawiki new aa wiki]

For earlier version - [AutomaticAnalysisIntroduction the older aa wiki]

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.

[:MriCro:dcm2nii] (part of MRICron) is a tool that allows manipulating DICOM images, including converting them to NIFTI/ANALYZE and the like, rotating and cropping images and anonymizing the image header. (The first function is particularly useful if you are an FSL user.)

Extensions to SPM/Matlab

  • 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

Scripts

There is a list of the people responsible for maintaining our scripts AvailableScripts.

General software

Programming

Other tools you might find useful

  • [:DumpDemographics:A script for dumping the age & sex of a list of CBU numbers]

  • ["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

CbuImaging: AnalysisSoftware (last edited 2013-03-07 21:24:01 by localhost)