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= Major neuroimaging software packages installed at the CBU = | = Software = You might want to [:ScientificComputing:read this overview of scientific computing] and keep up to date with this [:ImagingComputingDevelopments:list of latest software developments] |
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* [:SpmInformation:SPM] - the dominant software analysis package from the FIL in London. * [:FslInformation:FSL] ("fossil") - a powerful and fast collection of tools from FMRIB, Oxford |
== Major neuroimaging software packages installed at the CBU == Most imagers at the CBU use [:SpmInformation:SPM], the dominant software analysis package from the FIL in London, which runs under [:LearningMatlab:a language called Matlab]. However, [:FslInformation:FSL] ("fossil") - a powerful and fast collection of tools from FMRIB, Oxford, also has a following. For some applications (particularly flat mapping, or performing grey & white matter segmentation for MEG analysis) you might wish to use [:FreeSurferAnalysis:Freesurfer]. [:AfniInformation:Afni] is also installed. There is [:AvailableSoftware:a list of the people responsible for maintaining our neuroimaging (fMRI & MEG) software]. == Smaller tools == [:MriCro:MriCro and its successor MriCron] are a pair of very useful tools for viewing structural or functional images, producing 3D renderings of activation, and examining anatomical templates. == Extensions to SPM/Matlab == * [:AutomaticAnalysisIntroduction:aa - automatic analysis] - a system to automate SPM analyses, allowing the easy application of a set of pre-defined analysis recipes * MarsBar - a useful toolbox for performing region-of-interest (ROI) analyses * [:DataDiagnostics:tsdiffana] - data diagnostics utility, good for checking the quality of your fMRI data * SnpmInformation - for doing non-parametric statistics in SPM * LoadShare - our tool for balancing SPM jobs across machines * SpmBatchPrintContrasts - for printing contrasts automatically * DisplaySlices program for displaying multiple images slices in SPM == Beyond fMRI == * AnalyzingDiffusion * UsingFreesurfer = General computing = == Programming == * LearningUnix * LearningMatlab * LearningPython * ImageDataFormats == Other tools you might find useful == * [:UsingVNC Using VNC at the CBU] - gives you a graphical desktop on the linux machines from your desk * [:CbuSoftware:An archive of other software that you might find useful] == Useful tools in Linux == * gimp - Graphics viewing and editing program; the Linux version of Photoshop * acrobat - PDF viewer. * mozilla - web browser * nedit, gedit, emacs - text editors * kghostview - ps / psf / eps viewer useful for SPM postscript files |
Software
You might want to [:ScientificComputing:read this overview of scientific computing] and keep up to date with this [:ImagingComputingDevelopments:list of latest software developments]
Major neuroimaging software packages installed at the CBU
Most imagers at the CBU use [:SpmInformation:SPM], the dominant software analysis package from the FIL in London, which runs under [:LearningMatlab:a language called Matlab]. However, [:FslInformation:FSL] ("fossil") - a powerful and fast collection of tools from FMRIB, Oxford, also has a following.
For some applications (particularly flat mapping, or performing grey & white matter segmentation for MEG analysis) you might wish to use [:FreeSurferAnalysis:Freesurfer].
[:AfniInformation:Afni] is also installed.
There is [:AvailableSoftware:a list of the people responsible for maintaining our neuroimaging (fMRI & MEG) software].
Smaller tools
[:MriCro:MriCro and its successor MriCron] are a pair of very useful tools for viewing structural or functional images, producing 3D renderings of activation, and examining anatomical templates.
Extensions to SPM/Matlab
[:AutomaticAnalysisIntroduction:aa - automatic analysis] - a system to automate SPM analyses, allowing the easy application of a set of pre-defined analysis recipes
MarsBar - a useful toolbox for performing region-of-interest (ROI) analyses
[:DataDiagnostics:tsdiffana] - data diagnostics utility, good for checking the quality of your fMRI data
SnpmInformation - for doing non-parametric statistics in SPM
LoadShare - our tool for balancing SPM jobs across machines
SpmBatchPrintContrasts - for printing contrasts automatically
DisplaySlices program for displaying multiple images slices in SPM
Beyond fMRI
General computing
Programming
Other tools you might find useful
- [:UsingVNC Using VNC at the CBU] - gives you a graphical desktop on the linux machines from your desk
[:CbuSoftware:An archive of other software that you might find useful]
Useful tools in Linux
- gimp - Graphics viewing and editing program; the Linux version of Photoshop
- acrobat - PDF viewer.
- mozilla - web browser
- nedit, gedit, emacs - text editors
- kghostview - ps / psf / eps viewer useful for SPM postscript files