PyHRF: A Python Library for the Analysis of fMRI Data Based on Local Estimation of Hemodynamic Response Function

PyHRF: A Python Library for the Analysis of fMRI Data Based on Local Estimation of Hemodynamic Response Function

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Jaime Arias Almeida

December 07, 2017
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  1. 1.

    A Python Library for the Analysis of fMRI Data Based

    on Local Estimation of Hemodynamic Response Function J. Arias, P. Ciuciu, M. Dojat, F. Forbes, A. Frau-Pascual, T. Perret, J. M. Warnking
  2. 2.

    1. Introduction “Begin at the beginning”, the King said, very

    gravely, “and go on till you come to the end; then stop.” -- Lewis Carroll, Alice in Wonderland 2
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    × The current fMRI methods (e.g., SPM) estimates the neural

    activity using a canonical HRF for the whole brain. × There are local variations of the HRF in brain regions of patients with anomalies (e.g., Stenosis). Conjecture: Local variations of the HRF in patients with anomalies cause a wrong estimation of the neural activity. 3 Motivation
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    × Separate estimation of the response function (HRF) × A

    Bayesian framework allows to account for prior knowledge × A parcellation is used to deal with the HRF estimation regionally. JDE is solved with Variational Expectation Maximization (VEM). 4 Joint Detection-Estimation (JDE)
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    “Never send a human to do a machine’s job” --

    Agent Smith, The Matrix 5 2. PyHRF
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    6 PyHRF × Open source software × Pythonic × Robust

    scientific libraries × e.g., scipy, numpy, scikit-learn, nilearn, nipype ... × Implementation of several models × MCMC-BOLD, JDE-BOLD, JDE-ASL … × Parallel computation × Documentation, Notebooks, Docker image http://www.pyhrf.org https://github.com/pyhrf
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    8 PyHRF http://www.neurovault.org/images/307 Posterior Probability Map (PPM) Z-Scores Right Hand

    Gorgolewski, K. J., Storkey, A., Bastin, M. E., Whittle, I. R., Wardlaw, J. M., & Pernet, C. R. (2013). A test-retest fMRI dataset for motor, language and spatial attention functions. GigaScience, 2(1), 6. https://doi.org/10.1186/2047-217X-2-6
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    × Improvement of the PyHRF API for further developments ×

    Bring PyHRF to clinicians (GUI, CLI). × Pythonic framework from acquisition to visualization × Interaction SPM PyHRF Show the variations of the HRF response in brain regions of patients with anomalies (e.g., Stenosis). 9 Semavi Project
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    Alice: “How long is forever?” White Rabbit: “Sometimes, just one

    second. -- Lewis Carroll, Alice in Wonderland 13 3. Concluding Remarks 15 minutes
  11. 14.

    × PyHRF allows to estimate the HRF locally × Open

    source software × Multiplatform (Conda, Docker) × Extensible framework for the fMRI workflow Now we have a powerful tool for non-experts that will allow to test our hypothesis and new ideas. 14 Summary
  12. 15.

    × Continue to improve PyHRF × Internships × Use of

    PyHRF for the analysis of small animals × rats × Calibration of some parameters of the model to be able to compare our results with SPM × ROC analysis Show the variations of the HRF response in brain regions of patients with anomalies (e.g., Stenosis). 15 Future Work