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 *
 [wiki:LearningMatlab Matlab]. Useful for advanced work with SPM, and in understanding how SPM analyses neuroimaging data. Useful also for custom analyses with image data
 
 *
 [wiki:UsingSpm SPM] - Various guides on the theory and practice of SPM.
 
 *
 [wiki:UsingAnalyze AnalyzeAVW] - a comprehensive commercial program for viewing neuroimaging data. Particularly useful for rendering.
 
 *
 [[Anchor(mricro)]] Chris Rorden's [http://www.psychology.nottingham.ac.uk/staff/cr1/mricro.html MRIcro] - an excellent free, functional, and simple program for viewing neuroimages. It runs on Windows only.
 
  * [http://www.psychology.nottingham.ac.uk/staff/cr1/mritut.html MRIcro tutorial], with instructions on creating a region of interest, and prepare scans of damaged brains for spatial normalisation.
 
 *
 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
 * [http://www.mrc-cbu.cam.ac.uk/Imaging/Common/iv_volumetool.shtml iv_volumetool] - an image viewer from the PET group at the Université Catholique de Louvain, Belgium
 * [wiki:ImageViewer Viewer] - a simple matlab image viewer
 * [wiki: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://www.mrc-cbu.cam.ac.uk/Imaging/Common/pvconv.shtml pvconv] - a perl command line utility to convert [wiki:FormatBruker Bruker data format] to [wiki:FormatAnalyze Analyze image format]
 * [http://bishopw.loni.ucla.edu/AIR3/index.shtml AIR] - the Automated Image Realignment program, by Roger Woods
 *
 [wiki:Mpr mpr] - coregistration software, for matching MRIs to PET scans, CT scans etc in any combination. mpr is more robust than SPM for difficult coregistrations, including those where the brain is damaged.
 
 *
 [wiki:ReadingOnlineDocs Software and help on reading documents online] - such as Adobe Acrobat for pdf files and Ghostview for reading postcript (.ps) files.
 
Matthew Brett 7/10/99
== 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 [[mailto:olaf.hauk@mrc-cbu.cam.ac.uk|Olaf Hauk]] and [[mailto:johan.carlin@mrc-cbu.cam.ac.uk|Johan Carlin]].

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">Johan Carlin ||
||fMRIPrep ||<style="VERTICAL-ALIGN:top">[[https://fmriprep.org/en/stable/|website]], [[fMRIPrep|CBU information]] ||<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 ||
||dcm2bids (available through Neuroconda) ||<style="VERTICAL-ALIGN:top">[[https://github.com/jooh/Dcm2Bids|dcm2bids]] ||<style="VERTICAL-ALIGN:top">Johan Carlin ||
||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>>Johan Carlin ||
||FSL ||<style="VERTICAL-ALIGN:top">FslInformation ||<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 (FMRI)<<BR>> CbuMeg:SpmAnalysis (MEG/EEG) ||<style="VERTICAL-ALIGN:top">Rik Henson,<<BR>>Johan Carlin ||
||--(aa)-- deprecated ||<style="VERTICAL-ALIGN:top">[[AA|aa]] ||<style="VERTICAL-ALIGN:top">Daniel Mitchell,<<BR>>Johan Carlin ||
||Elekta Neuromag ||<style="VERTICAL-ALIGN:top">CbuMeg:NeuromagSoftware ||<style="VERTICAL-ALIGN:top">Olaf Hauk ||
||Matlab ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Johan Carlin,<<BR>>Rik Henson,<<BR>>Russell Thompson ||
||R ||<style="VERTICAL-ALIGN:top">http://www.r-project.org/ ||<style="VERTICAL-ALIGN:top">Dennis Norris,<<BR>> Rogier Kievit,<<BR>>Peter Watson ||
||Python ||<style="VERTICAL-ALIGN:top">[[http://www.r-project.org/|http://www.python.org/]] ||<style="VERTICAL-ALIGN:top">Dennis Norris,<<BR>>Johan Carlin ||
||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 ||
||node.js, npm, bids-validator ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Johan Carlin ||
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== Matlab ==
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.

== Imaging analysis packages ==
 * 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
 * MRIcro: see MriCro

== SPM toolboxes ==
 * MarsBar
 * SnpmInformation

== Other imaging software ==
 * [[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
 * ImageViewer - a simple matlab image viewer - now very old
 * [[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.

== 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.

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

Neuroconda

Github, CBU information

Johan Carlin

fMRIPrep

website, CBU information

Johan Carlin

scansync, ScannerSynch, MEGSynch

ScannerSynch

Johan Carlin

dcm2bids (available through Neuroconda)

dcm2bids

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 deprecated

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.

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 2020-12-01 15:32:50 by JohanCarlin)