Headache classification and automatic biomarker extraction from structural MRIs using deep learning

Md Mahfuzur Rahman Siddiquee, Jay Shah, Catherine Chong, Simona Nikolova, Gina Dumkrieger, Baoxin Li, Teresa Wu, Todd J. Schwedt

Research output: Contribution to journalArticlepeer-review


Data-driven machine-learning methods on neuroimaging (e.g. MRI) are of great interest for the investigation and classification of neurological diseases. However, traditional machine learning requires domain knowledge to delineate the brain regions first, followed by feature extraction from the regions. Compared with this semi-automated approach, recently developed deep learning methods have advantages since they do not require such prior knowledge; instead, deep learning methods can automatically find features that differentiate MRIs from different cohorts. In the present study, we developed a deep learning-based classification pipeline distinguishing brain MRIs of individuals with one of three types of headaches [migraine (n = 95), acute post-traumatic headache (n = 48) and persistent post-traumatic headache (n = 49)] from those of healthy controls (n = 532) and identified the brain regions that most contributed to each classification task. Our pipeline included: (i) data preprocessing; (ii) binary classification of healthy controls versus headache type using a 3D ResNet-18; and (iii) biomarker extraction from the trained 3D ResNet-18. During the classification at the second step of our pipeline, we resolved two common issues in deep learning methods, limited training data and imbalanced samples from different categories, by incorporating a large public data set and resampling among the headache cohorts. Our method achieved the following classification accuracies when tested on independent test sets: (i) migraine versus healthy controls - 75% accuracy, 66.7% sensitivity and 83.3% specificity; (2) acute post-traumatic headache versus healthy controls - 75% accuracy, 66.7% sensitivity and 83.3% specificity; and (3) persistent post-traumatic headache versus healthy controls - 91.7% accuracy, 100% sensitivity and 83.3% specificity. The most significant biomarkers identified by the classifier for migraine were caudate, caudal anterior cingulate, superior frontal, thalamus and ventral diencephalon. For acute post-traumatic headache, lateral occipital, cuneus, lingual, pericalcarine and superior parietal regions were identified as most significant biomarkers. Finally, for persistent post-traumatic headache, the most significant biomarkers were cerebellum, middle temporal, inferior temporal, inferior parietal and superior parietal. In conclusion, our study shows that the deep learning methods can automatically detect aberrations in the brain regions associated with different headache types. It does not require any human knowledge as input which significantly reduces human effort. It uncovers the great potential of deep learning methods for classification and automatic extraction of brain imaging-based biomarkers for these headache types.

Original languageEnglish (US)
Article numberfcac311
JournalBrain Communications
Issue number1
StatePublished - 2023


  • headache biomarkers
  • headache classification
  • migraine
  • persistent post-traumatic headache
  • post-traumatic headache

ASJC Scopus subject areas

  • Neurology
  • Psychiatry and Mental health
  • Biological Psychiatry
  • Cellular and Molecular Neuroscience


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