GingerALE Version 1.1
GingerALE is the BrainMap application that is used to perform an ALE meta-analysis on a group of coordinates or perform a comparison ALE meta-analysis on two groups of coordinates. 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. To this end, several modifications were made to the initial ALE algorithm, including a correction for multiple comparisons during the permutation test and a technique for comparing two ALE meta-analyses (Laird et al., 2005).
All output files are written in NIfTI (.nii) format. The input for a meta-analysis in GingerALE is a text file of your foci (generated by hand, from an excel worksheet, or as an export of your workspace in BrainMap Sleuth). To load these coordinates into GingerALE, go to File → Open Foci. The main window of GingerALE will then confirm for you the name of your foci file and the number of coordinates contained therein.
The ALE meta-analysis procedure follows 5 steps:
- ALE: This step computes the ALE values for each voxel in the brain in Talairach space.
- Permutation Testing: This step performs a permutation test to determine the null distribution of the ALE statistic at each voxel. We suggest using 5000 permutations. The output is an image of P values for each voxel. Note: this test is extremely computationally intensive.
- False Discovery Rate: This step takes the P values from above and computes the threshold for the ALE map using the FDR algorithm. The computation will yield two P value thresholds. The RIC generally uses thresholds returned by pN.
- Thresholding: This step creates the thresholded ALE map (final output). Select the image-wise P value (q, according to FDR theory), usually 0.05 or 0.01, and threshold the map that was output in step 1. Only voxels that were found to be statistically significant are assigned a value. The value that is written out is the computed ALE value. The thresholded map is output in .nii format and can be read by a number of functional neuroimaging software packages.
- Clusters: This step performs cluster analysis on the thresholded map. You must input the minimum volume that defines a cluster. Anatomical labels of cluster locations are provided by the Talairach Daemon.
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]
- Price_AllNaming.xml
- Price_CovertNamingSilentBaseline.xml
- Price_OvertNamingSilentBaseline.xml
- Price_CovertNamingSpeakingBaseline.xml
- Price_OvertNamingSpeakingBaseline.xml
- 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]