AnalysisSoftware - MRC CBU Imaging Wiki

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location: AnalysisSoftware

Neuroimaging software

You might want to read this overview of scientific computing.

Keep up to date with this list of latest developments

Try the student forum for helpful tips

Major neuroimaging software packages installed at the CBU

Most imagers at the CBU use 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 a language called Matlab allowing you to browse the source and write your own components relatively easily.

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 Freesurfer.

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 Brain Visa installed but I think it is probably an old version. If you find out, please put the latest information here!

There is 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 new aa wiki

For earlier version - [AutomaticAnalysisIntroduction the older aa wiki]

Smaller tools

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.

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

  • 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

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