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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. |
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| [:AfniInformation:Afni] is also installed. | [[FslInformation|FSL]] ("fossil") - a powerful and fast collection of open source tools from FMRIB, Oxford also has many strengths and has a substantial following. |
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| There is [:AvailableSoftware:a list of the people responsible for maintaining our neuroimaging (fMRI & MEG) software]. | 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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| = 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. |
[[AfniInformation|Afni]] is also installed. |
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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 |
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 == |
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| * [:DataDiagnostics:tsdiffana] - data diagnostics utility, good for checking the quality of your fMRI data | * [[DataDiagnostics|tsdiffana]] - data diagnostics utility, good for checking the quality of your fMRI data |
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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 read this overview of scientific computing.
Keep up to date with this list of latest developments
Try the student forum for helpful tips
Major neuroimaging software packages installed at the CBU
Most imagers at the CBU use 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 a language called Matlab allowing you to browse the source and write your own components relatively easily.
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 Freesurfer.
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 Brain Visa installed but I think it is probably an old version. If you find out, please put the latest information here!
There is 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 new aa wiki
For earlier version - [AutomaticAnalysisIntroduction the older aa wiki]
Smaller tools
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.
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
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
UsingVNC Using VNC at the CBU - gives you a graphical desktop on the linux machines from your desk
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