Brain Software

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See also

• Bibliography of Neuroinformatics
• Bibliography on Image registration
• Bibliography on Segmentation

Index

• Internet Analysis Tools Registry

Image Registration, spatial normalization

• AIR 5 and AIR 3 Automated Image Registration. Roger P. Woods programs. AIR allows automated registration of 3D (and 2D) images within and across subjects and within and sometimes across imaging modalities
  [C-source, UNIX, noncommercial]
• MRIWarp Non-linear 3D MRI warping program. Ulrik Kjems
  [C-source, UNIX, GPL license]

Analysis

• AFNI Analysis of Functional NeuroImages. R. W. Cox's program.
  [Unix+X11+Motif systems, Solaris, free for research use at nonprofit institutions]
• BrainVoyager Brain Innovation, Rainer Goebel.
  [Windows, Commercial]
• KUL_SPM KULeuven functions to automate SPM (fMRI) from MR Research Centre, Dept. Of radiology, University Hospitals, KULeuven.
  [Matlab]
• Lyngby Lyngby is a Matlab program package for the analysis of functional neuroimages.
  [Matlab, Free for non-commercial use]
• SPM Statistical Parametric Mapping. Package from Karl Friston and others from the Wellcome Department of Cognitive Neurology. The toolbox also includes image registration.
  [Matlab and C-source, UNIX/Windows, noncommercial]
• Yale fMRI Analysis Package by Pawel Skudlarski from Yale NMR research group.
  [Matlab]

Visualization

• BrainVoyager Brain Innovation, Rainer Goebel.
  [Windows, Commercial]
• Caret Computerized Anatomical Reconstruction and Editing Toolkit. Program by Heather Drury and David Van Essen of Washington University School of Medicine
  [UNIX-program, IRIX, noncommercial]
• GpetView Hiroshi Watabe's ANALYZE(tm) image viewer. From the homepage: "GpetView is light-weight image viewer based on Gtk+ library."
  [Unix (with Gtk+), free software (GNU)]
• mri3D (mri3dX) "mri3d is a general purpose program for 2 and 3-dimensional visualisation of structural MR images and functional localisations"
  Program of Krish Singh The program is part of the BrainTools package
  [Unix with Motif]
• MRIcro. Chris Rorden's medical image viewer, conversion tool, and region of interest editor.
  • Conversion: "Converts raw data, DICOM, ECAT, Interfile, NEMA, Genesis, Magnetom Vision or multivolume Analyze images to single volume [SPM friendly] Analyze format images."
  • Image viewing: "View Analyze format images (big or little endian)".
  • Other features see homepage
  [Windows 95/98/NT, freeware]
• Slice overlay. Matthew Brett's Image viewer.
  [Matlab, non-commercial]

	HBP	THOR Center for Neuroinformatics, Human Brain Project Repository (This server)
	THOR	THOR Center for Neuroinformatics
	ISP	Intelligent Digital Signal Processing
	IMM	Informatics and Mathematical Modelling
	DTU	Technical University of Denmark

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