Version 19 (modified by tjniskan, 7 years ago) (diff)


Aedes – A graphical tool for analyzing medical images



Aedes is an open source Matlab toolbox for analyzing medical images developed at the Biomedical NMR research group in A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland. It is mainly designed for region of interest (ROI) analysis and general visualization of magnetic resonance images but has also branched to various other purposes. Aedes runs under Windows, Linux and Mac OS X on Matlab 7.1 (R14SP3) and higher with image processing toolbox. Aedes is licensed under the GNU General Public License version 2.


  • MRI data import and export: Read support for NIfTI, Analyze, Varian FID and FDF, Bruker 2DSEQ and FID files, DICOM (through Image Processing Toolbox), S.M.I.S SUR and MRD, Gamma Medica SPECT/CT files, and Matlab MAT-files and workspace variables. Write support for NIfTI, Analyze and Matlab MAT-files. Support for arbitrary 2D, 3D or 4D matrices from the command line.
  • Region of interest (ROI) analysis: Drawing and manipulation of voxel based ROIs with export and import from and to NIfTI/Analyze/MAT formats. Comprehensive export of ROI statistics to Excel or text file.
  • Basic fMRI analysis: General linear model based fMRI analysis with FDR threshold estimation and some preprocessing functions (smoothing, high-pass filtering). Seed region based correlation mapping (resting-state fMRI). FMRI time series plotting from single voxels or ROIs.
  • MR parameter mapping: T1 (IR and SR), T1rho, T2, T2rho, apparent diffusion coefficient (ADC)
  • Data overlays: Overlaying of data from supported file formats or from workspace variable with transparency, thresholding and scaling.
  • Visualization: Export to many image formats (JPG, TIF, PNG, EPS) with ROIs and overlays.
  • Plug-in interface: A very easy-to-use plug-in interface for extending base functionality


  • First, download the latest revision of Aedes from the download page
  • Extract the archive to a folder of your choosing
  • Add two folders (<install folder>/aedes and <install folder>/aedes/misclib) to your Matlab search path
  • Open Aedes by entering the command aedes into the Matlab command window


Aedes is developed and maintained by

 Juha-Pekka Niskanen, MSc
 Department of Neurobiology
 A. I. Virtanen Institute
 University of Eastern Finland
 P.O. Box 1627
 FI-70211 Kuopio, FINLAND
 Email: juha-pekka.niskanen (at)

All rants, praises or questions about Aedes should be directed to the above address.

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