Diff for "AvailableSoftware" - MRC CBU Imaging Wiki
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This section explains which volunteers contribute their free time to maintaining and updating the following freeware packages. For all commercial software, please see the committee responsible for purchasing the 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.
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Manager: the person responsible for making sure that the software is as updated as users of this package require (often this is the most experienced/most vocal user). 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.
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Maintainer: the person responsible for performing updates to the software. General requests can be sent to members of the Methods group, including [[mailto:olaf.hauk@mrc-cbu.cam.ac.uk|Olaf Hauk]] and [[mailto:dace.apsvalka@mrc-cbu.cam.ac.uk|Dace Apšvalka]].
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Contributors: these persons are the people who offer updates to pieces of the software, but are not in charge of entire releases.
||||||||||<style="text-align:center;">'''Software at the CBU''' ||
||'''Package ''' ||<style="vertical-align:top;">'''Link ''' ||<style="vertical-align:top;">'''Contact ''' ||<style="vertical-align:top;">'''Versions ''' ||<style="vertical-align:top;">'''Comments ''' ||
||EEG Lab ||<style="vertical-align:top;"> ||<style="vertical-align:top;">Jason Taylor, Tristan Bekinschtein ||<style="vertical-align:top;"> ||<style="vertical-align:top;"> ||
||Fieldtrip ||<style="vertical-align:top;">FieldtripInformation and FieldtripAnalysis ||<style="vertical-align:top;">Olaf Hauk ||<style="vertical-align:top;"> ||<style="vertical-align:top;"> ||
||Freesurfer ||<style="vertical-align:top;">FreeSurferAnalysis ||<style="vertical-align:top;">Olaf Hauk ||<style="vertical-align:top;"> ||<style="vertical-align:top;"> ||
||FSL ||<style="vertical-align:top;">FslInformation ||<style="vertical-align:top;">Marta Correia ||<style="vertical-align:top;"> ||<style="vertical-align:top;"> ||
||Camino ||<style="vertical-align:top;"> ||<style="vertical-align:top;">Marta Correia ||<style="vertical-align:top;"> ||<style="vertical-align:top;"> ||
||Real Time MRI ||<style="vertical-align:top;"> ||<style="vertical-align:top;">Marta Correia, Daniel Mitchell ||<style="vertical-align:top;"> ||<style="vertical-align:top;"> ||
||MNE ||<style="vertical-align:top;">CbuMeg:MneAnalysis ||<style="vertical-align:top;">Olaf Hauk ||<style="vertical-align:top;">2.5/2.6/2.7.1 ||<style="vertical-align:top;"> ||
||SPM ||SpmInformation (FMRI) CbuMeg:SpmAnalysis (MEG/EEG) ||<style="vertical-align:top;">Rik Henson ||<style="vertical-align:top;"> ||<style="vertical-align:top;"> ||
||AA ||<style="vertical-align:top;"> ||<style="vertical-align:top;">Daniel Mitchell ||<style="vertical-align:top;"> ||<style="vertical-align:top;"> ||
||Elekta Neuromag ||<style="vertical-align:top">CbuMeg:NeuromagSoftware ||<style="vertical-align:top">Yury Shtyrov ||<style="vertical-align:top"> ||<style="vertical-align:top"> ||
||R ||<style="vertical-align:top">http://www.r-project.org/ ||<style="vertical-align:top">Dennis Norris ||<style="vertical-align:top"> ||<style="vertical-align:top"> ||
||Python ||<style="vertical-align:top"> ||<style="vertical-align:top">Dennis Norris ||<style="vertical-align:top"> ||<style="vertical-align:top"> ||
||C++ ||<style="vertical-align:top"> ||<style="vertical-align:top">Dennis Norris ||<style="vertical-align:top"> ||<style="vertical-align:top"> ||
||R ||<style="vertical-align:top"> ||<style="vertical-align:top">Dennis Norris ||<style="vertical-align:top"> ||<style="vertical-align:top"> ||
||E-Prime ||<style="vertical-align:top"> ||<style="vertical-align:top">Maarten van Casteren ||<style="vertical-align:top"> ||<style="vertical-align:top"> ||
||Presentation ||<style="vertical-align:top"> ||<style="vertical-align:top"> ||<style="vertical-align:top"> ||<style="vertical-align:top"> ||
||SPSS ||<style="vertical-align:top"> ||<style="vertical-align:top"> ||<style="vertical-align:top"> ||<style="vertical-align:top"> ||		 General IT requests should be sent to [[mailto:it-help@mrc-cbu.cma.ac.uk|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). <<BR>> <<BR>>
||||||||||<style="TEXT-ALIGN:center">'''Software at the CBU''' ||
||'''Package ''' ||<style="VERTICAL-ALIGN:top">'''Link ''' ||<style="VERTICAL-ALIGN:top">'''Contact ''' ||
||Neuroconda ||<style="VERTICAL-ALIGN:top">[[https://github.com/jooh/neuroconda|Github]], [[Neuroconda|CBU information]] ||<style="VERTICAL-ALIGN:top">Dace Apšvalka ||
||fMRIPrep ||<style="VERTICAL-ALIGN:top">[[https://fmriprep.org/en/stable/|website]], [[fMRIPrep|CBU information]] ||<style="VERTICAL-ALIGN:top">Dace Apšvalka ||
||scansync, !ScannerSynch, MEGSynch ||<style="VERTICAL-ALIGN:top">[[http://imaging.mrc-cbu.cam.ac.uk/mri/ScannerSynch|ScannerSynch]] ||<style="VERTICAL-ALIGN:top">Dace Apšvalka ||
||EEG Lab ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Fieldtrip ||<style="VERTICAL-ALIGN:top">FieldtripInformation<<BR>> FieldtripAnalysis ||<style="VERTICAL-ALIGN:top"><<BR>> Olaf Hauk ||
||Freesurfer ||<style="VERTICAL-ALIGN:top">FreeSurferAnalysis ||<style="VERTICAL-ALIGN:top">Kristjan Kalm,<<BR>> Marta Correia,<<BR>> Olaf Hauk,<<BR>>Dace Apšvalka ||
||FSL ||<style="VERTICAL-ALIGN:top">[[FslInformation|Fsl information]] ||<style="VERTICAL-ALIGN:top">Marta Correia ||
||Camino ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Marta Correia ||
||Real Time MRI ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Marta Correia,<<BR>>Daniel Mitchell ||
||MNE (-Python) ||<style="VERTICAL-ALIGN:top">[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_overview|MNE]] ||<style="VERTICAL-ALIGN:top">Olaf Hauk ||
||SPM ||[[SpmInformation|Spm information]] (FMRI)<<BR>> CbuMeg:SpmAnalysis (MEG/EEG) ||<style="VERTICAL-ALIGN:top">Rik Henson,<<BR>>Dace Apšvalka ||
||--(aa)-- deprecated ||<style="VERTICAL-ALIGN:top">[[AA|aa]] ||<style="VERTICAL-ALIGN:top">Daniel Mitchell ||
||Elekta Neuromag ||<style="VERTICAL-ALIGN:top">CbuMeg:NeuromagSoftware ||<style="VERTICAL-ALIGN:top">Olaf Hauk ||
||Matlab ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Dace Apšvalka,<<BR>>Rik Henson,<<BR>>Russell Thompson ||
||R ||<style="VERTICAL-ALIGN:top">http://www.r-project.org/ ||<style="VERTICAL-ALIGN:top">Dennis Norris,<<BR>> Dace Apšvalka,<<BR>>Peter Watson ||
||Python ||<style="VERTICAL-ALIGN:top">[[http://www.r-project.org/|http://www.python.org/]] ||<style="VERTICAL-ALIGN:top">Dennis Norris,<<BR>>Dace Apšvalka ||
||C++ ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Dennis Norris ||
||E-Prime ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Presentation ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||SPSS ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Peter Watson ||
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See 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|Learning Matlab]] for how to learn and use matlab. Matlab runs on all the unit imaging Linux machines.
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 * SPM: see SpmInformation for general information on SPM, and SpmVersions for instructions on running SPM at the CBU.
 * FSL: see FslInformation
 * AFNI: see AfniInformation
 * BrainVisa / Anatomist: see BrainVisaInformation
 * Freesurfer: FreesurferInformation		  * SPM: see [[SpmInformation|Spm Information]] for general information on SPM, and [[SpmVersions|Spm Versions]] for instructions on running SPM at the CBU.
 * FSL: see [[FslInformation|Fsl Information]]
 * AFNI: see [[AfniInformation|Afni Information]]
 * [[BrainVisa|Brain Visa]] / Anatomist: see [[BrainVisaInformation|Brain Visa Information]]
 * Freesurfer: [[FreesurferInformation|Freesurfer Information]]
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 * SnpmInformation  * [[SnpmInformation|Snpm Information]]
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 * [:UsingAnalyze: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:MRIcro] - start with `startmricro` on the Linux machines.
 * Krish Singh's [http://www.psychology.nottingham.ac.uk/staff/cr1/mri3dtut.html mri3d] - an excellent display tool, particularly for rendering of results onto brain surfaces.
 * [http://www.psychology.nottingham.ac.uk/staff/cr1/dicom.html freeware DICOM viewer and information], again for Windows, again by Chris Rorden		  * [[UsingAnalyze|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|MRIcro]] - start with `startmricro` on the Linux machines.
 * Krish Singh's [[http://www.psychology.nottingham.ac.uk/staff/cr1/mri3dtut.html|mri3d]] - an excellent display tool, particularly for rendering of results onto brain surfaces.
 * [[http://www.psychology.nottingham.ac.uk/staff/cr1/dicom.html|freeware DICOM viewer and information]], again for Windows, again by Chris Rorden
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 * [:Ana4Dto3D:ana4dto3d] - a tiny command line utility to convert Analyze 4D files to a series of 3D files, as well as byte swapping as required
 * [http://pvconv.sourceforge.net pvconv] - a perl command line utility to convert [:FormatBruker:Bruker data format] to [:FormatAnalyze:Analyze image format]
 * [http://www.fmrib.ox.ac.uk/fsl FSL] - the Oxford FMRIB software library for analyzing functional MRI and diffusion images.
 * See also [:ReadingOnlineDocs:Software and help on reading documents online] - such as Adobe Acrobat for pdf files and Ghostview for reading postcript (.ps) files.		  * [[Ana4Dto3D|ana4dto3d]] - a tiny command line utility to convert Analyze 4D files to a series of 3D files, as well as byte swapping as required
 * [[http://pvconv.sourceforge.net|pvconv]] - a perl command line utility to convert [[FormatBruker|Bruker data format]] to [[FormatAnalyze|Analyze image format]]
 * [[http://www.fmrib.ox.ac.uk/fsl|FSL]] - the Oxford FMRIB software library for analyzing functional MRI and diffusion images.
 * See also [[ReadingOnlineDocs|Software and help on reading documents online]] - such as Adobe Acrobat for pdf files and Ghostview for reading postcript (.ps) files.
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 * eog - convenient image viewer

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 Dace Apšvalka.

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

Neuroconda

Github, CBU information

Dace Apšvalka

fMRIPrep

website, CBU information

Dace Apšvalka

scansync, ScannerSynch, MEGSynch

ScannerSynch

Dace Apšvalka

EEG Lab

Fieldtrip

FieldtripInformation
FieldtripAnalysis


Olaf Hauk

Freesurfer

FreeSurferAnalysis

Kristjan Kalm,
Marta Correia,
Olaf Hauk,
Dace Apšvalka

FSL

Fsl information

Marta Correia

Camino

Marta Correia

Real Time MRI

Marta Correia,
Daniel Mitchell

MNE (-Python)

MNE

Olaf Hauk

SPM

Spm information (FMRI)
SpmAnalysis (MEG/EEG)

Rik Henson,
Dace Apšvalka

aa deprecated

aa

Daniel Mitchell

Elekta Neuromag

NeuromagSoftware

Olaf Hauk

Matlab

Dace Apšvalka,
Rik Henson,
Russell Thompson

R

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

Dennis Norris,
Dace Apšvalka,
Peter Watson

Python

http://www.python.org/

Dennis Norris,
Dace Apšvalka

C++

Dennis Norris

E-Prime

Presentation

SPSS

Peter Watson

Matlab

See our Beginner's pages for tutorials etc., or Learning Matlab 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 2023-02-14 12:28:48 by DaceApsvalka)