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| You might want to [:ScientificComputing:read this overview of scientific computing] and keep up to date with this [:ImagingComputingDevelopments:list of latest developments] | You might want to [[ScientificComputing|read this overview of scientific computing]]. |
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| Try the [:StudentForum:student forum for helpful tips] | Keep up to date with this [[ImagingComputingDevelopments|list of latest developments]] Try the [[StudentForum|student forum for helpful tips]] |
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| 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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| Most imagers at the CBU use [:SpmInformation:SPM, the dominant 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. |
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| [: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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| 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. |
[[AfniInformation|Afni]] is also installed. |
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| 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 in here! | 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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| There is [:AvailableSoftware:a list of the people responsible for maintaining our neuroimaging (fMRI & MEG) software]. | 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] |
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| [: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|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.) |
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| * [:AutomaticAnalysisIntroduction:aa - automatic analysis] - a system to automate SPM analyses, allowing the easy application of a set of pre-defined analysis recipes | |
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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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== Scripts == There is a list of the people responsible for maintaining our scripts AvailableScripts. |
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| * [: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] |
* [[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