Diff for "AvailableSoftware" - MRC CBU Imaging Wiki
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||!ScannerSynch, MEGSynch ||<style="VERTICAL-ALIGN:top">[[http://imaging.mrc-cbu.cam.ac.uk/mri/ScannerSynch|ScannerSynch]] ||<style="VERTICAL-ALIGN:top">Johan Carlin || ||scansync, !ScannerSynch, MEGSynch ||<style="VERTICAL-ALIGN:top">[[http://imaging.mrc-cbu.cam.ac.uk/mri/ScannerSynch|ScannerSynch]] ||<style="VERTICAL-ALIGN:top">Johan Carlin ||
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See our [[http://imaging.mrc-cbu.cam.ac.uk/meg/Beginners|Beginner's pages]] for tutorials etc., or LearningMatlab for how to learn and use matlab.

Matlab runs on all the unit imaging Linux machines as well as our Solaris machine, `navi` (see CbuComputingResources).

Linux machines l02-l07 run Matlab 6; machines l08-l13 Matlab 7.
See our [[http://imaging.mrc-cbu.cam.ac.uk/meg/Beginners|Beginner's pages]] for tutorials etc., or LearningMatlab for how to learn and use matlab. Matlab runs on all the unit imaging Linux machines.
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 * eog - convenient image viewer

Software for imaging at the CBU


Scientific software is managed by members of the imaging community (see below) and by members of the computing group. For queries concerning specific software packages, the people listed below are the best contact in the first instance.

On the linux compute cluster, scientific software packages are installed in /imaging/local/software/<package name>/, e.g. /imaging/local/software/fsl. These package directories contain sub-directories for each different version, and then sometimes sub-directories for specific architectures, e.g. /imaging/local/software/fsl/v5.0.8/x86_64 contains the 64 bit version of FSL 5.0.8.

General requests can be sent to members of the Methods group, including Olaf Hauk and Johan Carlin.

General IT requests should be sent to IT help. They will reach the whole IT team, who will decide what to do with them.

The following scientists volunteered to support particular scientific software packages. They can be contacted about computing-related problems, e.g. with respect to updates, missing libraries/toolboxes etc. (note: this does not include analysis support).

Software at the CBU




scansync, ScannerSynch, MEGSynch


Johan Carlin


Johan Carlin




Olaf Hauk



Kristjan Kalm,
Marta Correia,
Olaf Hauk,
Johan Carlin



Marta Correia


Marta Correia

Real Time MRI

Marta Correia,
Daniel Mitchell

MNE (-Python)


Olaf Hauk


SpmInformation (FMRI)
SpmAnalysis (MEG/EEG)

Rik Henson,
Johan Carlin



Daniel Mitchell,
Johan Carlin

Elekta Neuromag


Olaf Hauk


Johan Carlin,
Rik Henson,
Russell Thompson



Dennis Norris,
Rogier Kievit,
Peter Watson



Dennis Norris,
Johan Carlin


Dennis Norris




Peter Watson

node.js, npm, bids-validator

Johan Carlin


See our Beginner's pages for tutorials etc., or LearningMatlab for how to learn and use matlab. Matlab runs on all the unit imaging Linux machines.

Imaging analysis packages

SPM toolboxes

Other imaging software

  • AnalyzeAVW - a comprehensive commercial program for viewing neuroimaging data. Particularly useful for rendering. At the CBU, it will only run on the Solaris machines, if atall. Please contact MatthewBrett if you need this program.

  • Chris Rorden's MRIcro - start with startmricro on the Linux machines.

  • Krish Singh's mri3d - an excellent display tool, particularly for rendering of results onto brain surfaces.

  • freeware DICOM viewer and information, again for Windows, again by Chris Rorden

  • ImageViewer - a simple matlab image viewer - now very old

  • ana4dto3d - a tiny command line utility to convert Analyze 4D files to a series of 3D files, as well as byte swapping as required

  • pvconv - a perl command line utility to convert Bruker data format to Analyze image format

  • FSL - the Oxford FMRIB software library for analyzing functional MRI and diffusion images.

  • See also Software and help on reading documents online - such as Adobe Acrobat for pdf files and Ghostview for reading postcript (.ps) files.

Other general interest software available on the unit Linux machines

  • gimp - Graphics viewing and editing program; the Linux version of Photoshop
  • acrobat - PDF viewer.
  • mozilla - web browser
  • nedit, emacs - text editors
  • kghostview - ps / psf / eps viewer useful for SPM postscript files
  • eog - convenient image viewer

Many other packages are available from the menu in the bottom right of the windowing environments.

CbuImaging: AvailableSoftware (last edited 2018-06-11 08:58:41 by JohanCarlin)