GingerALE Version 2.1.1
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 map using the Tom Nichol’s FDR algorithm. Choose a False Discovery Rate (q) for the desired level of significance (e.g., 0.05 or 0.01). Also 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.
A command-line version of GingerALE is available for batch processing. For more information, please click here.
Sample Meta-Analysis Workspaces
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 .xml format:
- Laird AR, McMillan KM, Lancaster JL, Kochunov P, Turkeltaub PE, Pardo JV, Fox PT. A comparison of label-based review and activation likelihood estimation in the Stroop task. Hum Brain Mapp 25, 6-21, 2005. [pdf] [PubMed]
- Owen AM, McMillan KM, Laird AR, Bullmore E. N-back working memory paradigm: A meta-analysis of normative functional neuroimaging studies. Hum Brain Mapp 25, 46-59, 2005. [pdf] [PubMed]
- Glahn DC, Ragland JD, Abramoff A, Barrett J, Laird AR, Bearden CE, Velligan DI. Beyond hypofrontality: A quantitative meta-analysis of functional neuroimaging studies of working memory in schizophrenia. Hum Brain Mapp 25, 60-69, 2005. [pdf] [PubMed]
- Price CJ, Devlin JT, Moore CJ, Morton C, Laird AR. Meta-analyses of object naming: Effect of baseline. Hum Brain Mapp 25, 70-82, 2005. [pdf] [PubMed]
- Tan L-H, Laird AR, Li K, Fox PT. Neuroanatomical correlates of phonological processing of Chinese characters and alphabetic words: A meta-analysis. Hum Brain Mapp 25, 83-91, 2005. [pdf] [PubMed]
- Brown S, Laird AR, Ingham RJ, Ingham JC, Fox PT. Stuttered and fluent speech production: An ALE meta-analysis of functional neuroimaging studies. Hum Brain Mapp 25, 105-117, 2005. [pdf] [PubMed]