Differences between revisions 90 and 113 (spanning 23 versions)

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: see Spm Information for general information on SPM, and Spm Versions for instructions on running SPM at the CBU.
FSL: see Fsl Information
AFNI: see Afni Information
Brain Visa / Anatomist: see Brain Visa Information
Freesurfer: Freesurfer Information
MRIcro: see MriCro

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.

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+   ← Revision 113 as of 2023-02-14 12:28:48 → ⇥
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-Deletions are marked like this.
+Additions are marked like this.
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-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.
+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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-General requests can be sent to members of the Methods group, including [[mailto:olaf.hauk@mrc-cbu.cam.ac.uk|Olaf Hauk]] and [[mailto:tibor.auer@mrc-cbu.cam.ac.uk|Tibor Auer]].
+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:dace.apsvalka@mrc-cbu.cam.ac.uk|Dace Apšvalka]].
-Line 11:
+Line 13:
-||'''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">? ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Fieldtrip ||<style="VERTICAL-ALIGN:top">FieldtripInformation and FieldtripAnalysis ||<style="VERTICAL-ALIGN:top"><50%>Lucy MacGregor<<BR>>Olaf Hauk ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Freesurfer ||<style="VERTICAL-ALIGN:top">FreeSurferAnalysis ||<style="VERTICAL-ALIGN:top">Kristjan Kalm, Marta Correia, Olaf Hauk, Tibor Auer ||<style="VERTICAL-ALIGN:top">4.0.1/4.3.0/5.1.0 (glx only) ||<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, Tibor Auer ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||MNE (-Python) ||<style="VERTICAL-ALIGN:top">[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_overview|MNE]] ||<style="VERTICAL-ALIGN:top">Olaf Hauk ||<style="VERTICAL-ALIGN:top">2.5/2.6/2.7.1, MNE_Python ||<style="VERTICAL-ALIGN:top"> ||
||SPM ||SpmInformation (FMRI) CbuMeg:SpmAnalysis (MEG/EEG) ||<style="VERTICAL-ALIGN:top">Rik Henson, Tibor Auer ||<style="VERTICAL-ALIGN:top">12/8/5/2 ||<style="VERTICAL-ALIGN:top">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 ||<style="VERTICAL-ALIGN:top">[[AA]] ||<style="VERTICAL-ALIGN:top">Daniel Mitchell, Tibor Auer ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Elekta Neuromag ||<style="VERTICAL-ALIGN:top">CbuMeg:NeuromagSoftware ||<style="VERTICAL-ALIGN:top">Olaf Hauk ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
||Matlab ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Tibor Auer, Rik Henson, Russell Thompson ||<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">[[http://www.python.org/||<style="VERTICAL-ALIGN:top">Dennis|http://www.python.org]] ||<style="VERTICAL-ALIGN:top">Dennis Norris ||<style="VERTICAL-ALIGN:top"> ||
||C++ ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top">Dennis Norris ||<style="VERTICAL-ALIGN:top">4.1.2 ||<style="VERTICAL-ALIGN:top"> ||
||E-Prime ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||<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">Peter Watson ||<style="VERTICAL-ALIGN:top"> ||<style="VERTICAL-ALIGN:top"> ||
+||'''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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+Line 39:
-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|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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+ * eog - convenient image viewer

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