Conducting an ALE Meta-Analysis

1. Installation of GingerALE

Go to BrainMap to download the version of GingerALE for the operating system of the computer as a ZIP file.

Decompress the ZIP file. To avoid problems, decompress it within a local folder without blank spaces in its path.

Click the file GingerALE to execute the graphical interface of GingerALE.

2. Preparing Data for Meta-Analysis

Foci Formatting:

  • Create a text file with three columns for x, y, and z coordinates, separated by tabs or spaces.
  • Optionally, start the file with a line indicating the standard brain space (Talairach or MNI).
  • Separate foci groups with a line break, including identifying information such as the first author’s name, year, experiment name, or subject group name.
  • Include the number of subjects for each group and the coordinate data. Comments should start with "//".

3. Single Dataset Analysis

Loading Foci Data:

  • Open GingerALE and load your foci data using File > Open Foci.
  • GingerALE will read and verify the dataset, checking for mismatched reference spaces, missing subject sizes, and duplicated foci groups.
  • Review any errors or warnings displayed.

Performing ALE Analysis:

  • Once the data is loaded, choose threshold settings and begin the calculations.
  • The ALE meta-analysis follows four main steps: ALE scores, null distribution, thresholding, and cluster statistics.

4. Contrast Analyses

Running Separate ALE Analyses:

  • Perform separate ALE analyses on the two sets of foci.
  • Create a combined text file with foci from both files and run a pooled analysis. Ensure experiments appearing in both sets are only reported once.

Subtraction Analysis:

  • Select the “Contrast Studies” radio button in the main GingerALE window.
  • Open the three thresholded ALE images using the file menu items.
  • Verify settings for threshold method, number of permutations, and output file names, then click Compute.

5. Output Files

Types of Output Files:

  • ALE Image: Contains unthresholded ALE values for every voxel in the brain.
  • P Value Image: Contains unthresholded P values for each voxel.
  • Thresholded Image: ALE map thresholded at a given value, used as input for contrast analyses.
  • Cluster Image: Identifies contiguous non-zero regions in the thresholded image.
  • Cluster Spreadsheet: Provides detailed information about the resultant clusters, including volume, coordinates, and anatomical labels.
  • Data History: Contains parameters and output file names used in the analysis, along with additional information about different stages of the analysis.

6. Viewing Results

Using Mango for Visualization:

  • Download and install Mango from Mango.
  • Open the anatomical template file (Talairach or MNI) in Mango.
  • Add the thresholded results image as an overlay.
  • Update the image range to ensure all results are shown.
  • Enable anatomical labels and coordinates display for better interpretation.
  • Adjust the color map for better visualization of the results.

7. Additional Analysis Options

Connectivity Analyses:

Use meta-analytic connectivity modeling (MACM) to examine the functional connectivity of a specific brain region.

For more information: Robinson HBM 2010

For detailed instructions, refer to the full GingerALE user manual available in the BrainMap website: GingerALE Manual

VIDEO TUTORIAL: GingerALE Tutorial

Worflow

Image. Workflow stages of the activation likelihood estimation (ALE) method