• MR imaging is based on the behavior of atoms (most often – H, P, and Na) in the magnetic field
  • structures generating low signals are hypointense; structures generating high signals are hyperintense; tissues producing no signal are dark (blood, calcifications)
  • advantages over CT
    • high contrast and resolution, good visualization of pathologies in the posterior fossa
    • possibility of imaging in any plane (coronal, sagittal, oblique) and 3D reconstruction
    • possibility of non-contrast imaging of the cerebral arteries; contrast agents are used to visualize extracranial arteries
    • significant improvement in the acute stroke diagnosis using DWI, PWI, SWI, and GRE sequences
    • does not use ionizing radiation
  • disadvantages of MRI compared to CT
    • higher costs and longer examination times (typically lasting 30-60 minutes)
    • can be noisy, so earplugs or headphones are usually provided
    • difficulties with ventilated patients, as an MRI-compatible respirator must be available.
    • young children and uncooperative patients must be sedated or examined under general anesthesia (the risk of movement artifacts is substantial)
    • numerous MRI contraindications

Magnetic Resonance Imaging modalities



T1C+ (contrast-enhanced)

T1 fat suppressed

T1 fat-supressed sequence showing lipoma

T1C+ fat suppressed



T2 sequence with bright CSF




Cortical cerebral microbleeds and lobar hematomas in patient with cerebral amyloid angiopathy


Cerebral microbleeds on SWI (mixed pattern)


Acute ischema on DWI


ADC map

Diffusion tensor imaging (DTI) tractography

diffusion tensor imaging (DTI tractography
Flow sequences

CSF flow studies

CSF flow study
MR angiography

Bright blood

Non-contrast MRA (TOF)


MR venography (TOF)

MR venography (TOF)

Contrast-enhanced MRA

Contrast-enhanced MR angiography

Dark blood

Fast Spin Echo (FSE) Black Blood MRA

FSE dark blood MRA

Inversion Recovery (IR) Black Blood MRA

Susceptibility-weighted (SW) Black Blood MRI

SWI angiography
Vessel wall imaging

T1C+ black blood

Demonstration of ICA vasculitis using post-contrast high resolution MRI (HRMRI) (Obuses, 2014)


Perfusion weighted images (PWI)


Arterial Spin Labeling (ASL)


MR spectroscopy (MRS)
Basic MRI sequences (T1, T2, PD)
  • the principle of the method is the detection of T1 and T2 relaxation times (resulting in so-called T1 and T2-weighted images)
  • T1 is used for accurate anatomical imaging
    • water signal is low; fat is hyperintense
    • T1 signal is stronger when the relaxation time is shortened (e.g., due to the contrast agent) → T1C+
      • high-resolution MR T1 C+ dark blood sequence (see below) can be used to detect vasculitis  Vasculitis on MR T1C+ black blood sequence
    • fat suppression techniques can be used to improve the contrast between different tissues by suppressing the signal from fat  → see here
      • CHESS (Fat-Sat)
      • STIR
  • T2 – better detection of lesions containing more water
    • FLAIR sequence is used for water suppression (the CSF is dark, and periventricular lesions can be better distinguished)
    • CHESS (Fat-Sat) is used to suppress fat
  • PD (proton density) – image quality depends on the density of hydrogen protons in the tissues. Compared to other sequences, it is less useful in CNS diagnostics
Magnetic resonance imaging (MRI)
bone, calcifications
water, CSF
gadolinium bright bright
air dark dark dark
Diffusion-weighted images (DWI)
  • DWI visualizes impaired (restricted) diffusion of water molecules (or protons) caused by the energetic failure of Na+/K+ membrane pumps
  • it is highly sensitive and specific (88-100%) for detecting acute cerebral infarction within minutes of its onset, with a maximum of 4-6 hours
  • acute ischemia appears hyperintense (bright) on DWI (b factor around 1000 s/mm2) and hypointense (dark) on calculated ADC (apparent diffusion coefficient) maps
    • ADC <620×10-3 mm/s is likely to identify ischemia
    • following recanalization, an increase in signal intensity is often observed on ADC maps within the ischemic area    After recanalization, there is often an increase in ADC at the site of ischemia (visible on both DWI and FLAIR) [Albers]
  • DWI changes are not specific to ischemia – they can occur in any impairment of transport mechanisms (edema). Such changes are often reversible, and lesions are not hypointense on the ADC map)
  • artifacts can occur on DWI due to its dependence on the T2 signal
    • increased T2 signal can lead to T2 shine through and T2 washout   
    • reduced T2 signal leads to the T2 blackout phenomenon (hypointense on DWI)
MR DWI in stroke
Corpus callosum infarction and intraventricular hemorrhage
Perfusion-weighted images (PWI)
  • PWI provides information about the current blood supply to the brain tissue by measuring the passage of gadolinium-based contrast agent (GBCA) through the brain tissue
  • after bolus administration of GBCAs, the same parameters as for CT perfusion (CBV, CBF, MTT, TTP) can be obtained
  • tissue with impaired perfusion (↑ MTT) comprises infarction (core, approx. corresponding to DWI lesion), the penumbra and also the area of benign oligemia. The difference between the area of  impaired perfusion and diffusion approximately determines the size of the penumbra (PWI/DWI mismatch)
PWI-DWI mismatch
Gradient-echo sequence (GRE)
  • paramagnetic substances appear dark (calcification, blood, metals)
  • GRE reliably detects both recent and old bleeding, including cerebral microbleeds  Acute ICH and SAH on MR GRE
    • can detect acute ICH (initially, only a dark rim may be visible), SAH, or subtle hemorrhagic complications in ischemic stroke  ⇒ GRE should be included in emergency brain MR studies  (Kidwell, 2004)
    • characteristics of hyperacute hematoma:
      • T1 isointense
      • T2/FLAIR – isointense or mildly hyperintense
      • GRE hypointense (initially only hypointense rim + core of heterogenous signal intensity due to the diamagnetic oxyhemoglobin)
      • DWI hyperintense, ADC hypointense
    • GRE outperforms CT in the detection of old hemorrhages
  • GRE allows the detection of intra-arterial and intravenous thrombi (blooming artifact)   MCA thrombus on MR SWI The left transverse and sigmoid sinus thrombosis The straight sinus thrombosis on GRE
    • in addition to dural sinus thrombosis, it can help to detect smaller veins thrombosis
    • both the dense artery sign and the blooming artifact are common in erythrocyte-rich thrombi  [Liebeskind, 2011]]
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Susceptibility-weighted images (SWI)
  • SWI is particularly sensitive to paramagnetic substances, such as oxyhemoglobin, deoxyhemoglobin, and methemoglobin, as well as iron deposits
  • advantages and disadvantages:
    • high-quality images with excellent spatial resolution outperforming GRE (may detect small abnormalities that may not be visible on other MRI sequences)
    • long acquisition time
    • limited contrast
  • SWI is used to detect a variety of abnormalities in the brain (similar to GRE):
    • acute thrombus detection Distal MCA thrombus on MR SWI
      • thrombus is hypointense on MR SWI (deoxyhemoglobin)
      • SWI offers high sensitivity to detect thrombi in distal segments (where it often outperforms MRA)
    • detection of venous thrombosis
      • hypointense signal in affected veins and vessels
      • stasis and enlargement in the surrounding veins  Thrombosis of the left transverse sinusu with the dilatation of surrounding the veins (left image). Normalization after successful recanalization (right image)
    • prediction of hemorrhagic transformation
      • detection of cerebral microbleeds – up to 6x more sensitive than conventional gradient sequences (their presence increases the risk of bleeding during thrombolysis or anticoagulant therapy)   Cerebral microbleeds on SWI (mixed pattern)
      • early detection of hemorrhagic transformation (higher sensitivity compared to CT and MR GRE)
Arterial Spin Labeling (ASL)
  • ASL is a technique that measures cerebral blood flow (CBF) using water in arterial blood as an endogenous contrast agent; CBF maps are created
    • this is done by using a magnetic field gradient to temporarily alter the direction of the protons’ spin, which makes them visible to the MRI scanner. After a short period, the labeled protons pass through the brain and are detected by the MRI scanner
  • advantages:
    • non-invasive perfusion imaging
    • high sensitivity (because it measures the passage of labeled protons through the brain rather than relying on the accumulation of a tracer)
    • reproducibility – ASL results are highly reproducible, making it a valuable tool for research and clinical practice
  • disadvantages:
    • ASL seems to overestimate perfusion lesion compared to PWI
    • lower spatial resolution compared to PET/SPECT (may not be able to detect small changes in CBF)
    • susceptibility to motion artifacts
    • technical challenges (ASL requires a high-field MRI scanner and specialized software)
  • useful in these indications:
    • acute stroke/TIA
    • chronic cerebrovascular diseases 
    • degenerative diseases (AD, FTD)
    • brain tumors
    • migraine (hyperperfusion) Migraine attack with hyperperfusion on MRI ASL
    • posterior reversible encephalopathy (PRES) Subacute PRES (MR ASL)
Contrast-enhanced MRI
  • contrast agents are substances injected into the bloodstream to enhance the visibility of certain structures in MRI images Gadolinium-based contrast agents (GBCAs) enhance pathological lesions on MRI
    • may improve the visibility of lesions that are not visible on non-enhanced images
    • may help distinguish between different types of tissues
  • contrast agents facilitate proton relaxation, which shortens the T1 and T2 relaxation times
    • a shortening of the T1 relaxation time leads to an increase in signal intensity, while a shortening of the T2 relaxation time leads to a decrease in signal intensity
  • contrast agents can be divided into paramagnetic and super-paramagnetic agents
    • paramagnetic substances amplify the magnetic field, resulting in a shortening of the relaxation time. They have a wide range of applications and are often used in CNS examinations because of their ability to penetrate damaged BBB – Magnevist (gadopentetate), Omniscan (gadodiamide), Dotarem (Gd-DOTA, gadoteric acid)
    • super-paramagnetic agents are solid substances that are introduced into the body as suspensions and are very effective in shortening the relaxation times of protons
  • contrast agents are associated with a risk of adverse events and increased costs

MRI and acute stroke diagnosis

  • DWI – essential in the early detection of cerebral ischemia, can be included at the beginning of the examination protocol  Acute ischemic stroke on MRI - 36h from onset, clinical presentation with the right hand monoparesis
  • T1, T2, FLAIR – usually negative in the acute stage of stroke, changes on FLAIR (cytotoxic edema) appear within 3-4 hours
    • DWI/FLAIR mismatch can guide the management of patients with an unclear time of onset of stroke (WAKE-UP, MR WITNESS)
  • GRE
    • detection of bleeding, including recent hemorrhagic infarction
    • detection of venous or arterial thrombi, characterized by a “blooming artifact
  • MRA – time-of-flight (TOF) technique is used for examination of intracranial arteries to detect occlusion (exclude artifacts)
  • MR perfusion – helps in identifying the penumbra, the potentially salvageable tissue surrounding an ischemic core
  • MR SWI – highly sensitive in detecting early hemorrhagic infarction or thromboembolism (high sensitivity even for peripheral segments)
Acute (0-7 days)
  • marked hyperintensity on DWI and hypointensity on ADC images
  • early DWI reversal may occur after reperfusion; in most cases, it represents DWI pseudonormalization
Subacute (7-21 days)
  • ADC pseudonormalization occurs after 5-7 days; ADC values rise and return near the baseline; later continue to rise (ischemia becomes hyperintense¨)
  • DWI remains hyperintense (due to T2 shine-through)
Chronic ( >3 weeks)
  • ADC signal is increased
  • DWI signal decreases (as T2 shine-through is resolved)
ADC pseudonormalisation around day 5-7 after the stroke onset

MRI angiography (MRA)

MRA techniques

Dark Blood MRA → see here
(vascular imaging strategy where the signal from flowing blood is suppressed – rendering it “black”)

  • Fast Spin Echo (FSE) Black Blood MRA
  • Inversion Recovery (IR) Black Blood MRA
  • Susceptibility-weighted (SW) Black Blood MRI

Bright Blood MRA

  • Contrast-enhanced MRA
  • Non-contrast MRA
    • Time-of-Flight (TOF)
    • Phase-contrast (PC)
    • Steady-state Free Precession (SSFP)
    • Fast Spin Echo (FSE)
    • Arterial Spin Labeling (ASL)

MRA applications

Intracranial arteries

  • TOF (Time Of Flight) method, without contrast agent administration MRA 3D TOF
    • evaluates only flow, false-positive findings are common
    • sufficient to show occlusions/stenoses of major arteries   MCA stenosis on MRA (M1 segment)  TOF showing right PCA occlusion (green arrow) and right MCA stenosis (red arrow)
    • low sensitivity for peripheral occlusions
  • SWI dark blood sequence detects thrombi thanks to blooming artifact MCA thrombus on MR SWI
  • T1C+ dark blood sequence helps to detect inflammatory changes in the vessel wall  Demonstration of ICA vasculitis using post-contrast high resolution MRI (HRMRI) (Obuses, 2014) Vasculitis on T1C+ black blood sequence

Extracranial arteries

  • contrast-enhanced MRA (CE-MRA) for extracerebral vessels  Carotid artery stenoses on MRA
  • the stenosis should be measured according to NASCET criteria
  • MRA may overestimate stenosis compared to DSA (pseudo-occlusion)

MR venography

ICA stenosis on MRA

MCA occlusion

Transverse sinus thrombosis

MRI and dissection diagnosis

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MRI and intracranial hemorrhage

  • the paramagnetic properties of hemoglobin derivatives are responsible for the MRI signal changes
  • imaging depends on the degree and extent of hemoglobin conversion within the coagulum (see the table)
    • in the acute stage of hemorrhage, the finding in T1,2 is non-specific
    • subsequently, as oxyhemoglobin converts to deoxyhemoglobin (peaking around day 2), a characteristic decrease in T2 signal intensity is observed
    • in the following days, methemoglobin levels rise, causing the lesion to become hyperintense (mainly in T1 and PD)
    • ~  2-4 weeks later, a rim of low signal intensity appears in T2, corresponding to hemosiderin in macrophages
  • gradient echo sequence (GRE) can also detect early bleeding with similar sensitivity to CT, allowing MRI to be used as an initial imaging method in the acute stroke setting Acute ICH and SAH on MR GRE  [Lin, 2001]
    • GRE is more sensitive than CT for detecting old bleeding and is equally effective for detecting hemorrhagic infarction [Renou, 2010]
    • does not effectively differentiate between hemorrhagic infarction and ICH
    • hemorrhage is hyperintense in the hyperacute and late subacute stages, hypointense in the acute, early subacute, and chronic stages [Kang, 2001]
    • mean ADC ratio is  0.70-0.73 in early stages and 2.56 in chronic stages [Kang, 2001]
    • in ischemia, the ADC lesion typically becomes hyperintense around day 30; with hemorrhage, hypointensity persists for over 100 days [Ebisu, 1997]
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Magnetic Resonance Imaging (MRI)
link: https://www.stroke-manual.com/magnetic-resonance-imaging-mri/