Help Needed with NiMARE MACM Analysis - Code Modification and Runtime

Software Support
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Summary of what happened:

I am currently facing an issue while using NiMARE for MACM analysis, and I would greatly appreciate your assistance. Following the tutorial available [here] (NiMARE: Neuroimaging Meta-Analysis Research Environment — NiMARE 0.0.8+0.ged4abc4.dirty documentation) , specifically in the “MKDA Chi2 with FWE correction” section, I encountered an error during the execution of the following code:

mkda = nimare.meta.MKDAChi2(kernel__r=10)
mkda.fit(dset_sel, dset_unsel)

corr = nimare.correct.FWECorrector(method="montecarlo", n_iters=1000)
cres = corr.transform(mkda.results)

The error message I received was ‘MKDAChi2’ object has no attribute ‘results.’ To address this, I modified the code from mkda.fit(dset_sel, dset_unsel) to mkda.results = mkda.fit(dset_sel, dset_unsel). This resolved the error, but the line of code seems to run for an extended period, approximately six to seven hours.

I have a couple of questions:

  1. Is my modification to the code correct, changing from mkda.fit(dset_sel, dset_unsel) to mkda.results = mkda.fit(dset_sel, dset_unsel)?
  2. Is the runtime of six to seven hours normal for the given configuration: Macbook Pro 2017, 2.3GHz Dual-core Intel Core i5? Approximately how much time does it typically take to complete the entire process?

I would be grateful for any insights or suggestions regarding this matter. Thank you in advance for your time and assistance.

Best regards,
Yaya

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It looks like you’re following an older tutorial. I would recommend matching the documentation you follow with the version of the software you’re using. The .results attribute was removed from MetaEstimator objects in version 0.0.12, so you must have a NiMARE version >=0.0.12 installed.

I wouldn’t modify the MetaEstimator object. Instead, I would recommend creating a new variable results (e.g., results = mkda.fit(dset_sel, dset_unsel)).

That sounds about right. Running MKDAChi2 Monte Carlo permutations will, unfortunately, take a long time. You can increase the number of cores you use (n_cores) to speed things up. I can’t predict how long the whole process should take, but two recommendations I would make are (1) increase the number of iterations to 10000 for a publication-quality meta-analysis and (2) run it on a high-performance cluster.

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Thank you very much !

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Just so you know, @adelavega recent made some modifications to MKDAChi2 that I think should both speed it up and reduce memory usage (see Add `sum_across_studies` to kda by adelavega · Pull Request #859 · neurostuff/NiMARE · GitHub and Optimize compute_kda_ma for memory and speed by adelavega · Pull Request #857 · neurostuff/NiMARE · GitHub). Please consider trying out the newest release (0.2.1).

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@Yaya_Jiang Yes, this new version should speed things up about 3x on a single processor, but also reduces memory by around 20x, which means you can run on more cores in parallel even on a laptop. Try it!

I would also say that for first pass results, you could use FDRCorrector, which would be almost instant.

For montecarlo, there’s just no getting around that even something that takes 20s x 10,000 iterations = 55 hours of computation (single core), unfortunately. So I would also reccomend a HPC for “final” publication level results.

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