Command-Line GingerALE

The command-line tools match the computational steps in the graphical version of GingerALE: ALE, Thresholding and Cluster Analysis. Each step requires GingerALE.jar

ALE & Testing Significance:

java -cp GingerALE.jar org.brainmap.meta.getALE2

Required Parameters:

File Name Parameters: (Optional)

Threshold Method Parameters: (Optional)

Cluster Size Parameters: (Optional)

Other Parameters: (Optional)

ALE Contrast:

java -cp GingerALE.jar org.brainmap.meta.getALE2Contrast

Required parameters:

Optional parameters:

Cluster Analysis for non-GingerALE images

Use this step to create a "cluster image" which is required in the cluster analysis step.

java -cp GingerALE.jar org.brainmap.meta.getClustersOnly

Required parameters:

Optional parameters:

Cluster Analysis

java -cp GingerALE.jar org.brainmap.meta.getClustersStats

Required parameters:

Optional parameters:

Mask Options

Mask images and the Talairach label image are saved as NIfTI images within GingerALE.jar. The mask options are:

  1. Talairach, More Conservative: "Tal_wb.nii"
  2. Talairach, Less Conservative: "Tal_wb_dil.nii"
  3. MNI, More Conservative: "MNI_wb.nii"
  4. MNI, Less Conservative: "MNI_wb_dil.nii"

"WB" refers to "whole brain", as these masks cover both gray and white matter. The more conservative options are smaller; the less conservative options have been dilated ("dil") by 2mm.

For example:

java -cp GingerALE.jar org.brainmap.meta.getALE2  
   example_foci.txt -mask=MNI_wb.nii

If you use BrainMap Sleuth to create your text file of foci data, and you use one of our masks, then each command-line step will double-check the reference spaces and give you a warning message if they don't match.

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