= 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 == * AnalyzingDiffusion * UsingFreesurfer == Scripts == There is a list of the people responsible for maintaining our scripts AvailableScripts. = General software = == Programming == * LearningUnix * LearningMatlab * LearningPython * ImageDataFormats == 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