Note: For miscellaneous code snippets and tips please see the Scripts and Tricks page of the NISOx website.

Professor Thomas Nichols and the NISOx group have contributed towards the development of two neuroimaging software analysis programs, FSL & SPM.

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• FSL stands for FMRIB's Software Library, and is a product of the analysis group at Oxford University's Centre for Functional Magnetic Resonance Imaging of the Brain. FSL is a collection of C++ programs sewed together with bash scripts and tcl/tk GUIs.

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• SPM stands for Statistical Parametric Mapping, and is the product of the methods group at University College London's Wellcome Trust Centre for Neuroimaging ("The FIL"). SPM is a collection of Matlab scripts and Matlab-linked C code.

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In addition Prof. Thomas Nichols also has created and contributed towards several distinct add-on toolboxes. These include the following:

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• Randomise
  The component of FSL that provides nonparametric permutation-based inference.

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• SnPM
  A toolbox for SPM provides nonparametric permutation-based inference.

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• DSE
  A toolbox for variance decomposition of 4D data sets in order to diagnose spatio-temporal corruptions.

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• FDR
  A more powerful approach to multiple testing (was an extension, now integrated into SPM).

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• SwE
  An SPM extension for longitudinal and repeated measures data.

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• NINGA
  A toolbox implementing fast and powerful genome wide association analysis of dense genetic data with high dimensional imaging phenotypes.

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• FPHI
  A toolbox for Heritability Inference for Related Subjects Based on Neuroimaging Phenotypes.

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• BSGLMM
  A toolbox implementing the Bayesian Spatial Generalised Linear Mixed Model.

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• BHPGM
  A toolbox implementing the Bayesian Hierarchical Poisson Gamma Model.

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• BHICP
  A toolbox implementation of Bayesian Hierarchical Independent Cox Processes.

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• APACE
  A tool for fast heritability inference.

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OLD! These projects are no longer supported

• SPMd
  A toolbox for SPM that provides assumption-checking and data exploration tools.

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• PCT
  A toolbox for SPM that provides Percent Change Threshold images.

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In addition, for extra code excerpts, snippets and tips, please refer to the NISOx blog and the Scripts and Tricks section of the NISOx website.