- Download the GingerALE command line jar file.
- Try the following. This should run the meta-analysis with cluster-level correction and log the time it took to run. I don't know how to measure memory usage though.
start_time=$(date +%s)
java -cp GingerALE.jar org.brainmap.meta.getALE2 \
/Users/taylor/Documents/tsalo/ohbm2021-nimare-tutorial/data/meta-analysis/Laird2015_faces_MNI.txt \
-mask=MNI_wb.nii -p=0.001 -perm=10000 -fwe=0.05
end_time=$(date +%s)
# elapsed time with second resolution
elapsed=$(( end_time - start_time ))
echo $elapsed
- Run the same meta-analysis with NiMARE. We probably need to extract the MNI_wb mask for this to work.
- Compare the cluster maps.
- I guess calculate the Dice coefficient between the thresholded and binarized statistical maps. Is that all? How do we determine what a good result is? We could try running the correction procedure multiple times with different random seeds, but neither tool currently has a method for setting a random seed. We could hack it with NiMARE by just setting the seed before running the script, but I don't know if there's a similar solution for GingerALE.
