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.

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

Package

Link

Contact

ScannerSynch, MEGSynch

ScannerSynch

Johan Carlin

EEG Lab

Fieldtrip

FieldtripInformation
FieldtripAnalysis


Olaf Hauk

Freesurfer

FreeSurferAnalysis

Kristjan Kalm,
Marta Correia,
Olaf Hauk,
Johan Carlin

FSL

FslInformation

Marta Correia

Camino

Marta Correia

Real Time MRI

Marta Correia,
Daniel Mitchell

MNE (-Python)

MNE

Olaf Hauk

SPM

SpmInformation (FMRI)
SpmAnalysis (MEG/EEG)

Rik Henson,
Johan Carlin

aa

aa

Daniel Mitchell,
Johan Carlin

Elekta Neuromag

NeuromagSoftware

Olaf Hauk

Matlab

Johan Carlin,
Rik Henson,
Russell Thompson

R

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

Dennis Norris,
Rogier Kievit,
Peter Watson

Python

http://www.python.org/

Dennis Norris,
Johan Carlin

C++

Dennis Norris

E-Prime

Presentation

SPSS

Peter Watson

node.js, npm, bids-validator

Johan Carlin

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

Other general interest software available on the unit Linux machines

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