Command-Line GingerALE
The command-line tools match the steps in the graphical version of GingerALE: ALE, Thresholding and Cluster Analysis. Each step requires GingerALE.jar or the slightly smaller version ale.jar
ALE & Testing Significance:
java -cp GingerALE.jar org.brainmap.meta.getALE2
Required parameters:
- Foci_Text, the text file of foci data to use
Optional parameters:
- -mask=Mask_Image, the NIfTI image to use as a mask
Defaults to Talairach, More Conservative (more) - -ale=ALE_Prefix, file name for the output NIfTI image of ALE values
Defaults to foci name + "_ALE.nii" - -pval=PVal_Prefix, file name for the output NIfTI image of P values
Defaults to foci name + "_PVal.nii"
Thresholding
java -cp GingerALE.jar org.brainmap.meta.getThreshold2
Required parameters:
- ALE_Image, the NIfTI image of ALE values from the previous step
- PVal_Image, the NIfTI image of P values from the previous step
- FDR_Value, the false discovery rate, a floating point value like 0.05
Optional parameters:
- -pID, flag to use pID in the FDR step
- -noDiagonals, flag to use more strict clustering algorithm
- -min=Min_Vol_MM, an integer value for the minimum cluster size to allow
Defaults to 1 mm3 - -mask=Mask_Image, the NIfTI image to use as a mask
Defaults to Talairach, More Conservative (more) - -thresh=Thresholded_Image_Prefix, file name for the output NIfTI image of thresholded ALE values
Defaults to ALE_Image file name + "_thresh.nii" - -clust=Cluster_Image_Prefix, file name for the ouput NIfTI image of clusters
Defaults to ALE_Image file name + "_clust.nii"
Cluster Analysis
java -cp GingerALE.jar org.brainmap.meta.getClustersStats
Required parameters:
- Foci_Text, the original text file of foci data
Used to create experiment tables - ALE_Image, the original or thresholded ALE values
Used to find weighted centers and extrema - Clust_Image, the NIfTI image of clusters from the previous step
Optional parameters:
- -mni, flag to transform locations to Talairach before looking up Talairach labels
- -limitExtrema, flag to remove local extrema from statistics
- -label=Talairach_Image, NIfTI image of Talairach labels
Defaults to talairach.nii, which is included in GingerALE.jar like the masks - -out=Output_Prefix, the file name prefix for text (.txt) and spreadsheet (.xls) output files
Defaults to Foci_Text file name + "_clust"
Masks, etc
Mask images and the Talairach label image are saved as NIfTI images within GingerALE.jar. The mask options are:
- Talairach, More Conservative: "new_mask_smaller.nii"
- Talairach, Less Conservative: "new_mask_bigger.nii"
- MNI, More Conservative: "Colin27_smaller.nii"
- MNI, Less Conservative: "Colin27_bigger.nii"
java -cp GingerALE.jar org.brainmap.meta.getALE2 example_foci.txt -mask=Colin27_smaller.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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