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| Keep up to date with this [:ImagingComputingDevelopments:list of latest software developments] | = Neuroimaging software = You might want to [:ScientificComputing:read this overview of scientific computing]. |
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| = Major neuroimaging software packages installed at the CBU = | Keep up to date with this [:ImagingComputingDevelopments:list of latest developments] |
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| 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. | Try the [:StudentForum:student forum for helpful tips] |
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| For some applications (particularly flat mapping, or performing grey & white matter segmentation for MEG analysis) you might wish to use [:FreeSurferAnalysis:Freesurfer]. | == Major neuroimaging software packages installed at the CBU == Most imagers at the CBU use [:SpmInformation:SPM, the predominant software analysis package from the FIL in London], which has consistently been on the cutting edge of new methods. It runs under [:LearningMatlab:a language called Matlab] allowing you to browse the source and write your own components relatively easily. [:FslInformation:FSL] ("fossil") - a powerful and fast collection of open source tools from FMRIB, Oxford also has many strengths and has a substantial following. For some applications (particularly generating inflated brains, flat mapping, or performing grey & white matter segmentation for MEG analysis) you might wish to use [:FreeSurferAnalysis:Freesurfer]. |
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| There are some old licenses for Brain Voyager around. This point-and-click commercial package has many impressive features. It seems we might have [:BrainVisaInformation:Brain Visa] installed but I think it is probably an old version. If you find out, please put the latest information here! |
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| = 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. |
== Automatic analysis (aa) == A system to automate SPM analyses, allowing the easy application of a set of pre-defined analysis recipes |
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| = Extensions to SPM/Matlab = * [:AutomaticAnalysisIntroduction:aa] - a system to automate SPM analyses, allowing the easy application of a set of pre-defined analysis recipes |
For version 3.0 and later - the [http://www.cambridgeneuroimaging.com/aawiki new aa wiki] For earlier version - [AutomaticAnalysisIntroduction the older aa wiki] == 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. [:MriCro:dcm2nii] (part of MRICron) is a tool that allows manipulating DICOM images, including converting them to NIFTI/ANALYZE and the like, rotating and cropping images and anonymizing the image header. (The first function is particularly useful if you are an FSL user.) == Extensions to SPM/Matlab == |
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| * SpmBatchPrintContrasts - for printing contrasts automatically * DisplaySlices program for displaying multiple images slices in SPM |
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| = General computing = | == Scripts == There is a list of the people responsible for maintaining our scripts AvailableScripts. = General software = |
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| * [wiki:UsingVNC Using VNC at the CBU] - gives you a graphical desktop on the linux machines from your desk | * [:DumpDemographics:A script for dumping the age & sex of a list of CBU numbers] * ["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] |
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| * kghostview - ps / psf / eps viewer useful for SPM postscript files | * kghostview - ps / psf / eps viewer useful for SPM postscript files |
Neuroimaging software
You might want to [:ScientificComputing:read this overview of scientific computing].
Keep up to date with this [:ImagingComputingDevelopments:list of latest developments]
Try the [:StudentForum:student forum for helpful tips]
Major neuroimaging software packages installed at the CBU
Most imagers at the CBU use [:SpmInformation:SPM, the predominant software analysis package from the FIL in London], which has consistently been on the cutting edge of new methods. It runs under [:LearningMatlab:a language called Matlab] allowing you to browse the source and write your own components relatively easily.
[:FslInformation:FSL] ("fossil") - a powerful and fast collection of open source tools from FMRIB, Oxford also has many strengths and has a substantial following.
For some applications (particularly generating inflated brains, flat mapping, or performing grey & white matter segmentation for MEG analysis) you might wish to use [:FreeSurferAnalysis:Freesurfer].
[:AfniInformation:Afni] is also installed.
There are some old licenses for Brain Voyager around. This point-and-click commercial package has many impressive features.
It seems we might have [:BrainVisaInformation:Brain Visa] installed but I think it is probably an old version. If you find out, please put the latest information here!
There is [:AvailableSoftware:a list of the people responsible for maintaining our neuroimaging (fMRI & MEG) software].
Automatic analysis (aa)
A system to automate SPM analyses, allowing the easy application of a set of pre-defined analysis recipes
For version 3.0 and later - the [http://www.cambridgeneuroimaging.com/aawiki new aa wiki]
For earlier version - [AutomaticAnalysisIntroduction the older aa wiki]
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.
[:MriCro:dcm2nii] (part of MRICron) is a tool that allows manipulating DICOM images, including converting them to NIFTI/ANALYZE and the like, rotating and cropping images and anonymizing the image header. (The first function is particularly useful if you are an FSL user.)
Extensions to SPM/Matlab
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
Scripts
There is a list of the people responsible for maintaining our scripts AvailableScripts.
General software
Programming
Other tools you might find useful
[:DumpDemographics:A script for dumping the age & sex of a list of CBU numbers]
- ["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