= 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//, 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]]. 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). <
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> ||||||||||'''Software at the CBU''' || ||'''Package ''' ||'''Link ''' ||'''Contact ''' || ||Neuroconda ||[[https://github.com/jooh/neuroconda|Github]], [[Neuroconda|CBU information]] ||Dace Apšvalka || ||fMRIPrep ||[[https://fmriprep.org/en/stable/|website]], [[fMRIPrep|CBU information]] ||Dace Apšvalka || ||scansync, !ScannerSynch, MEGSynch ||[[http://imaging.mrc-cbu.cam.ac.uk/mri/ScannerSynch|ScannerSynch]] ||Dace Apšvalka || ||EEG Lab || || || ||Fieldtrip ||FieldtripInformation<
> FieldtripAnalysis ||<
> Olaf Hauk || ||Freesurfer ||FreeSurferAnalysis ||Kristjan Kalm,<
> Marta Correia,<
> Olaf Hauk,<
>Dace Apšvalka || ||FSL ||[[FslInformation|Fsl information]] ||Marta Correia || ||Camino || ||Marta Correia || ||Real Time MRI || ||Marta Correia,<
>Daniel Mitchell || ||MNE (-Python) ||[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_overview|MNE]] ||Olaf Hauk || ||SPM ||[[SpmInformation|Spm information]] (FMRI)<
> CbuMeg:SpmAnalysis (MEG/EEG) ||Rik Henson,<
>Dace Apšvalka || ||--(aa)-- deprecated ||[[AA|aa]] ||Daniel Mitchell || ||Elekta Neuromag ||CbuMeg: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.r-project.org/|http://www.python.org/]] ||Dennis Norris,<
>Dace Apšvalka || ||C++ || ||Dennis Norris || ||E-Prime || || || ||Presentation || || || ||SPSS || ||Peter Watson || == Matlab == 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. == Imaging analysis packages == * 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]] * MRIcro: see MriCro == SPM toolboxes == * MarsBar * [[SnpmInformation|Snpm Information]] == 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.