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A Hybrid 3DCNN and 3DC-LSTM Based Model for 4D Spatio-Temporal fMRI Data: An ABIDE Autism Classification Study

  • Ahmed El-GazzarEmail author
  • Mirjam Quaak
  • Leonardo Cerliani
  • Peter Bloem
  • Guido van Wingen
  • Rajat Mani Thomas
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11796)

Abstract

Functional Magnetic Resonance Imaging (fMRI) captures the temporal dynamics of neural activity as a function of spatial location in the brain. Thus, fMRI scans are represented as 4-Dimensional (3-space + 1-time) tensors. And it is widely believed that the spatio-temporal patterns in fMRI manifests as behaviour and clinical symptoms. Because of the high dimensionality (\(\sim \)1 Million) of fMRI, and the added constraints of limited cardinality of data sets, extracting such patterns are challenging. A standard approach to overcome these hurdles is to reduce the dimensionality of the data by either summarizing activation over time or space at the expense of possible loss of useful information. Here, we introduce an end-to-end algorithm capable of extracting spatiotemporal features from the full 4-D data using 3-D CNNs and 3-D Convolutional LSTMs. We evaluate our proposed model on the publicly available ABIDE dataset to demonstrate the capability of our model to classify Autism Spectrum Disorder (ASD) from resting-state fMRI data. Our results show that the proposed model achieves state of the art results on single sites with F1-scores of 0.78 and 0.7 on NYU and UM sites, respectively.

Keywords

Deep learning ASD 3D convolutions 3D convolutional-LSTM rs-fMRI 

Notes

Acknowledgement

This work was supported by the Netherlands Organization for Scientific Research (NWO; 628.011.023), Philips Research, AAA Data Science Program, and ZonMW (Vidi; 016.156.318).

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Ahmed El-Gazzar
    • 1
    Email author
  • Mirjam Quaak
    • 1
    • 2
  • Leonardo Cerliani
    • 1
  • Peter Bloem
    • 2
  • Guido van Wingen
    • 1
  • Rajat Mani Thomas
    • 1
  1. 1.Department of PsychiatryAmsterdam UMC, University of AmsterdamAmsterdamThe Netherlands
  2. 2.Vrije Universiteit AmsterdamAmsterdamThe Netherlands

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