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anbai106 / mlni

Machine Learning in NeuroImaging (MLNI) is a python package that performs various tasks using neuroimaging data.
https://anbai106.github.io/mlni/
MIT License
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Run pyHYDRA without covariate_tsv #2

Closed IoannaSkampardoni closed 3 years ago

IoannaSkampardoni commented 3 years ago

Hi. While running pyHYDRA without covariate_tsv, an error appears at the base.py line which normally reads the covariates file. From the error message 'ValueError: Invalid file path or buffer object type: <class 'int'>', I think it tries to read the covariates file but there is no such file. I attach a screenshot. Thank you. Read covariates file

anbai106 commented 3 years ago

Hi, n_threads is an optional argument (so does covariate_tsv). You gave it as mandatory. That's why pyHYDRA take n_threads as covariate_tsv, leading to your ValueError.

Please run this: clustering(feature_tsv, output_dir, k_min, k_max, cv_repetition, n_threads=n_threads)

Thanks

IoannaSkampardoni commented 3 years ago

Great, thank you!