NiMARE: get_studies_by_label failing
Summary
NameError: name ‘get_studies_by_label’ is not defined
Additional details
- NiMARE version: 0.0.11
- python 3.6
What were you trying to do?
Using terms to filter papers and doing a meta-analysis
What did you expect to happen?
Get the ids of the filtered papers
What actually happened?
Function ‘get_studies_by_label’ can not be found, which is given on the website of NiMARE.
Reproducing the bug
# Use neurosynth database
dset = Dataset.load("neurosynth_dataset_with_abstracts.pkl.gz")
#define target variables
ids = get_studies_by_label(labels='(child* | adolescen*) & (trauma* | maltreat* | abuse | advers* | neglect)', label_threshold=0.001)
dset_sel = dset.slice(ids)
print(len(ids))
#do meta-analysis with ALE
from nimare.meta.cbma.ale import ALE
meta = ALE()
results = meta.fit(dset_sel)
corr = FWECorrector(method="montecarlo", n_cores=8)
cres = corr.transform(results)
plot_stat_map(
results.get_map("z"),
cut_coords=[0, 0, -8],
draw_cross=False,
cmap="RdBu_r",
threshold=0.1,
)
plot_stat_map(
cres.get_map("z_desc-size_level-cluster_corr-FWE_method-montecarlo"),
cut_coords=[0, 0, -8],
draw_cross=False,
cmap="RdBu_r",
threshold=0.1,
)
I tried to do the same thing on NiMARE as I did on NeuroSynth but it reported errors. If the function ‘get_studies_by_label’ did not work, how could I filter papers by terms?
About this issue
- Original URL
- State: closed
- Created 2 years ago
- Comments: 18 (8 by maintainers)
Thank you for your patience! You solved all my questions! What an amazing man you are!
Using the method of list.intersection,it combines schizophrenia(700+)and childhood (1100+), and gets a total of 44 ids. I’ll give some more information tomorrow to figure out what’s wrong.