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.
- MATLAB 7.5 (or newer).
- Requires the Tools for NIfTI and ANALYZE Images package from the Matlab Exchange
- 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 (email@example.com)