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:
- Foci_Text, the text file of foci data to use
File Name Parameters: (Optional)
- -mask=Mask_Image, the NIfTI image to use as a mask
- Defaults to Talairach, More Conservative (more)
- -ale=Name, file name for the output NIfTI image of ALE values
- Defaults to foci name + "_ALE.nii"
- -pval=Name, file name for the output NIfTI image of P values
- Defaults to foci name + "_PVal.nii"
- -thresh=Name, file name for the thresholded ALE values
- Defaults to foci name + description of chosen threshold method
- Thresholded ALE images are only saved if a method is chosen.
Threshold Method Parameters: (Optional)
- -p=Value, Uncorrected P value threshold
- -pN=Value, FDR pN corrected P value threshold
- -pID=Value, FDR pID corrected P value threhsold
- -perm=Integer, number of permutations
- Use only with permutation-based methods: FWE & Cluster-Level
- -fwe=Value, Family-wise Error
- Permutation-based: requires -perm parameter
- -clust=Value, Cluster-Level Inference
- Permutation-based: requires -perm parameter
- Requires "cluster forming" secondary threshold method
For example: -p, -pN, -pID
Cluster Size Parameters: (Optional)
- -minVol=Integer, Minimum allowed volume in mm^3
- -minRecommended, Chooses the volume as a fraction of total volume
Other Parameters: (Optional)
- -nonAdd, change the ALE method to the non-additive method described in Turkeltaub, HBM 2011
- -noPVal, create only an ALE image, no P value or thresholded images
ALE Contrast:
java -cp GingerALE.jar org.brainmap.meta.getALE2Contrast
Required parameters:
- ALE_1, the thresholded ALE image of data set 1
- ALE_2, the thresholded ALE image of data set 2
- ALE_Pooled, the thresholded ALE image of combined data sets 1 & 2
Optional parameters:
- -mask=Mask_Image, the NIfTI image to use as a mask
- Defaults to Talairach, More Conservative (more)
- -out1=Set1_Output_Prefix, shortened name used in output files when referring to data set 1
- -out2=Set2_Output_Prefix, shortened name used in output files when referring to data set 2
- -foci1=Set1_Foci_Text, input foci for data set 1 (foci are usually embedded in GingerALE output images)
- -foci2=Set2_Foci_Text, input foci for data set 2
- -foci3=Pooled_Foci_Text, combined input foci for data set 1 & 2
- -nonadd, flag to change the ALE method to the non-additive method described in Turkeltaub, HBM 2011
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:
- Input_Image, the thresholded NIfTI image to be clustered
Optional parameters:
- -min=Volume: the minimum volume in mm3 allowed in the cluster image - defaults to 1 mm3
- -out=Name: the output file name for the cluster image
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"
Mask Options
Mask images and the Talairach label image are saved as NIfTI images within GingerALE.jar. The mask options are:
- Talairach, More Conservative: "Tal_wb.nii"
- Talairach, Less Conservative: "Tal_wb_dil.nii"
- MNI, More Conservative: "MNI_wb.nii"
- 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.