GingerALE Version 3.0.2
GingerALE is the BrainMap application that is used to perform an ALE meta-analysis on coordinates in Talairach or MNI space. GingerALE can also be used to convert coordinates between MNI and Talairach spaces using the icbm2tal transform.
The ALE meta-analysis method was initially developed by Peter Turkeltaub (Turkeltaub et al., 2002). This method of meta-analysis was adopted by BrainMap in 2003. Several modifications have been made to the ALE algorithm since then, and the current version of our software is reported in Eickhoff et al., 2009.
All output files are written in NIfTI (.nii) format. The input for a meta-analysis in GingerALE is a text file of your foci. Foci can be generated by hand, from an excel worksheet, or as an export of your workspace in BrainMap Sleuth, matching this format. To load these coordinates into GingerALE, go to File → Open Foci. The main window of GingerALE will then confirm the number of coordinates and experiments in your file.
The ALE meta-analysis procedure follows 3 steps:
- ALE and Testing Significance: GingerALE computes the ALE values for each voxel in the brain and performs a test to determine the null distribution of the ALE statistic at each voxel.
- Thresholding: GingerALE takes the P values from the previous step and computes the threshold for the ALE image. Choose a direct P-value threshold or a permutation-based Family-wise Error, using either voxel values or cluster sizes. With thresholds other than cluster-based FWE, you can choose a minimum cluster size in mm3. This step creates the thresholded ALE map that is output in .nii format and can be read by a number of functional neuroimaging software packages.
- Cluster Analysis: GingerALE performs cluster analysis on the thresholded map, based on the minimum volume that is specified in the previous step. Anatomical labels of final cluster locations are provided by the Talairach Daemon.
FHWM Values
Please note that the FWHM is calculated by the number of subjects in each experiment, as described by Eickhoff et al., 2009.
| Subjects | FWHM (mm) |  |
|---|---|---|
| 1 | 19.07 | |
| 2 | 14.74 | |
| 3 | 12.98 | |
| 4 | 12.00 | |
| 5 | 11.37 | |
| 6 | 10.94 | |
| 10 | 10.00 | |
| 15 | 9.50 | |
| 28 | 9.01 | |
| 50 | 8.75 | |
| 195 | 8.50 | |
| Infinity | 8.41 |
Command-Line GingerALE
A command-line version of GingerALE is available for batch processing. For more information, please click here.
Sample Meta-Analysis Data
In May 2005, the journal Human Brain Mapping published a Special Issue on Meta-Analysis of Functional Brain Mapping (Volume 25, Issue 1). Sleuth workspaces of selected meta-analyses presented in this issue are available.
In 2009, the American Journal of Psychiatry published "Prefontal activation deficits during episodic memory in schizophrenia". Example result files are available in NIfTI format and a spreadsheet describing the significant regions.