Shed – Automated parcellation of functional activation maps


Shed is designed to perform automated sub-division of a statistical map into regions derived from the topology of the map. The Watershed algorithm is used to identify separable peaks from within contiguous super-threshold clusters. The program is written in Matlab and provides a graphical user interface to select input files and operating parameters. It is specifically intended for use with first- or second-level activations maps from functional MRI studies. The program reads and writes 3D NIFTI format images.


Shed works in the following manner:

  • An activation map, and optional underlay anatomical image, are loaded by the user
  • Using statistical and extent thresholds, the activation maps is divided into standard clusters
  • The Watershed algorithm is used to divide clusters into regions with separable peak sub-regions
  • A label image is saved to disk along with a print-out of region statistics
  • Shed is implemented through a GUI with no user intervention (i.e. no hand drawing).
  • Reads and writes 3D NIFTI format images.
  • Implements user-selectable settings for threshold, extent, neighboring voxel definition, and others options
  • Displays the results in the GUI for user inspection.
Installation Instructions
  • Download the .zip file (see Downloading section below).
  • Unzip the files and add them to your Matlab Path.
  • For Linux or Mac, copy the file shed.fig.LINUX to shed.fig.
  • For Windows, copy the file shed.fig.WINDOWS to shed.fig.
  • Be sure that you have the Tools for NIfTI and ANALYZE Images folder in your Matlab path.
  • Run Matlab and type shed at the prompt to bring up the Shed GUI.

The Shed program is available here in a .zip bundle: Download Shed (version 3) – updated 03/22/2019 (includes a bug fix for Windows where images were not displaying)

  • Load an activation map by clicking the Activation Map… button. Select a NIFTI file (extension .nii)
  • Load an optional anatomical image with the same voxel dimensions by clicking on the Struct Image… button.
  • Click the GO button to run the program
  • A manual for Shed remains to be written…

For comments or questions on the Shed program, send e-mail to Mark Elliott (