Hi Taylor and NiMARE community,
I have some questions regarding the outputs.I have run a coordinate-based ALE,then I try to use the function “get_clusters_table” to get the outputs.I found a lot of NaN in the “Peak Stat” column.I wonder if there are any other ways to get the similar table of outputs as “get_clusters_table” ?
Besides,when I want to use siibra to convert the outputs of NiMARE,but I don’t know whether it is suitable or not?
pip install git+https://github.com/FZJ-INM1-BDA/siibra-python.git@main
import siibra
atlas = siibra.atlases.MULTILEVEL_HUMAN_ATLAS
with siibra.QUIET: # suppress progress output
julich_pmaps = atlas.get_map(
space=“mni152”,
parcellation=“julich”,
maptype=“continuous”
)
point = siibra.Point((0, 58, 16), space=‘mni152’)
with siibra.QUIET: # suppress progress output
assignments = julich_pmaps.assign(point)
assignments.sort_values(by=[‘MaxValue’], ascending=False)
Nilearn’s get_clusters_table can sometimes identify a center of mass outside of the actual cluster, in which case you end up with that NaN value. If you’re comfortable writing Python code, you could maybe clone Nilearn and edit the get_clusters_table function to identify the closest voxel within the cluster. Otherwise, a good workaround might be to just open the map in a viewer like Mango and just select a voxel in the relevant cluster to see what the statistic is.
