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||Fieldtrip ||<style="VERTICAL-ALIGN:top">FieldtripInformation and FieldtripAnalysis ||<style="VERTICAL-ALIGN:top">Lucy !MacGregor
Olaf Hauk ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Fieldtrip ||<style="VERTICAL-ALIGN:top">FieldtripInformation and FieldtripAnalysis ||<style="VERTICAL-ALIGN:top">Lucy !MacGregor, Olaf Hauk ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||

Software for imaging at the CBU

Software

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.

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

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

Package

Link

Contact

Versions

Comments

EEG Lab

?

Fieldtrip

FieldtripInformation and FieldtripAnalysis

Lucy MacGregor, Olaf Hauk

Freesurfer

FreeSurferAnalysis

Kristjan Kalm, Marta Correia, Olaf Hauk, Tibor Auer

4.0.1/4.3.0/5.1.0 (glx only)

FSL

FslInformation

Marta Correia

Camino

Marta Correia

Real Time MRI

Marta Correia, Daniel Mitchell, Tibor Auer

MNE (-Python)

MNE

Olaf Hauk

2.5/2.6/2.7.1, MNE_Python

SPM

SpmInformation (FMRI) SpmAnalysis (MEG/EEG)

Rik Henson, Tibor Auer

12/8/5/2

Default latest version of SPM8 is FIL official release r4667. There is also a devel SVN version available with local changes. Older versions of SPM5 and SPM2 available.

AA

AA

Daniel Mitchell, Tibor Auer

Elekta Neuromag

NeuromagSoftware

Olaf Hauk

Matlab

Tibor Auer, Rik Henson, Russell Thompson

R

http://www.r-project.org/

Dennis Norris

Python

[[http://www.python.org/||<style="VERTICAL-ALIGN:top">Dennis|http://www.python.org]]

Dennis Norris

C++

Dennis Norris

4.1.2

E-Prime

Presentation

SPSS

Peter Watson

Matlab

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 as well as our Solaris machine, navi (see CbuComputingResources).

Linux machines l02-l07 run Matlab 6; machines l08-l13 Matlab 7.

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

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

CbuImaging: AvailableSoftware (last edited 2023-02-14 12:28:48 by DaceApsvalka)