Diff for "AnalysisSoftware" - MRC CBU Imaging Wiki
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You might want to [:ScientificComputing:read this overview of scientific computing]. You might want to [[ScientificComputing|read this overview of scientific computing]].
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Keep up to date with this [:ImagingComputingDevelopments:list of latest developments] Keep up to date with this [[ImagingComputingDevelopments|list of latest developments]]
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Try the [:StudentForum:student forum for helpful tips] 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. 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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[:FslInformation:FSL] ("fossil") - a powerful and fast collection of open source tools from FMRIB, Oxford also has many strengths and has a substantial following. [[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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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]. 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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[: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 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]].
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For version 3.0 and later - the [http://www.cambridgeneuroimaging.com/aawiki new aa wiki] For version 3.0 and later - the [[http://www.cambridgeneuroimaging.com/aawiki|new 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.
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[: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.) [[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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 * [: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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 * [: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]
 * [[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]]

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

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

CbuImaging: AnalysisSoftware (last edited 2013-03-07 21:24:01 by localhost)