Is a computed tomography (CT) brain scan superior to a magnetic resonance imaging (MRI) brain scan for diagnosing headaches?

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Last updated: October 19, 2025View editorial policy

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MRI vs CT for Headaches

MRI is generally superior to CT for evaluating headaches in most clinical scenarios, except in emergency settings where CT is preferred for detecting acute blood products such as subarachnoid hemorrhage. 1, 2

Primary Headaches (Migraine, Tension, Cluster)

  • Neuroimaging (either MRI or CT) is not usually warranted in patients with primary headaches who have normal findings on neurological examination 2
  • The prevalence of significant intracranial abnormalities in patients with primary headaches and normal neurological examinations is extremely low (approximately 0.2%), making routine imaging unnecessary 2
  • When imaging is performed for primary headaches, the yield is generally low:
    • In a study of 449 children with headache, only <1% had relevant findings to explain their headaches 1
    • Similar findings have been reported in adult populations 3

When Neuroimaging Should Be Considered

Neuroimaging should be considered in patients with:

  • Unexplained abnormal findings on neurological examination (Grade B recommendation) 1, 2
  • Atypical headache features or "red flags" including:
    • Headache worsened by Valsalva maneuver 1, 4
    • Headache that awakens the patient from sleep 1, 4
    • New-onset headache in older patients 1, 4
    • Progressively worsening headache 1, 4
    • Rapid increase in headache frequency 1, 4
    • Thunderclap headache (sudden severe headache) 1
    • Headache with focal neurological symptoms 4

MRI vs CT Comparison

When MRI is Superior:

  • MRI is the imaging modality of choice when there are signs of increased intracranial pressure or concern for possible tumor 1
  • MRI provides superior characterization of:
    • Brain parenchymal lesions 5
    • Vascular malformations (after initial detection) 5
    • Soft tissue abnormalities 6
    • Posterior fossa pathology 2
    • Encephalitis (using T2 FLAIR, diffusion-weighted imaging, and contrast sequences) 1

When CT is Superior:

  • CT is superior for detecting acute subarachnoid hemorrhage (sensitivity of 98% vs variable sensitivity of MRI) 1, 2
  • CT is preferred in emergency settings with suspected intracranial bleeding 1, 5
  • CT is faster and more readily available in acute settings 1
  • CT doesn't require screening for metallic implants and is suitable for patients with contraindications to MRI 7
  • CT is often preferred in the acute trauma setting 6

Special Considerations

  • "Sinus headache" is a common misdiagnosis among migraine sufferers, and neuroimaging is not indicated for this presumptive diagnosis 2
  • In children with headaches, CT is usually not the study of choice except in emergency settings 1
  • For suspected brain tumors in emergency settings where MRI is not possible, CT without IV contrast can be performed initially, followed by contrast-enhanced studies if needed 1

Common Pitfalls to Avoid

  • Ordering neuroimaging for reassurance without clinical indications (low yield and not cost-effective) 2, 3
  • Misdiagnosing migraine with cranial autonomic symptoms as "sinus headache" 1
  • Failing to recognize red flags that warrant neuroimaging 4
  • Using CT when MRI would provide better characterization of suspected pathology 5
  • Using MRI when CT would be more appropriate for detecting acute hemorrhage 1

Remember that the decision to perform neuroimaging should be guided by clinical presentation, and testing should be avoided if it will not lead to a change in management 2.

References

Guideline

Guideline Directed Topic Overview

Dr.Oracle Medical Advisory Board & Editors, 2025

Guideline

Diagnostic Imaging for Migraine Headaches

Praxis Medical Insights: Practical Summaries of Clinical Guidelines, 2025

Research

Neuroimaging for the evaluation of chronic headaches: an evidence-based analysis.

Ontario health technology assessment series, 2010

Research

The radiology of headache.

The Medical clinics of North America, 1991

Research

Appropriate use of neuroimaging in headache.

Current pain and headache reports, 2015

Professional Medical Disclaimer

This information is intended for healthcare professionals. Any medical decision-making should rely on clinical judgment and independently verified information. The content provided herein does not replace professional discretion and should be considered supplementary to established clinical guidelines. Healthcare providers should verify all information against primary literature and current practice standards before application in patient care. Dr.Oracle assumes no liability for clinical decisions based on this content.

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