Magnetic Resonance Imaging (MRI) of the Brain and Spine: Basics

Magnetic resonance imaging (MRI) is one of the most commonly used tests in neurology and neurosurgery. MRI provides exquisite detail of brain, spinal cord and vascular anatomy, and has the advantage of being able to visualize anatomy in all three planes: axial, sagittal and coronal (see the example image below).

Axial - Sagittal - Coronal Views

MRI has an advantage over CT in being able to detect flowing blood and cryptic vascular malformations. It can also detect demyelinating disease, and has no beam-hardening artifacts such as can be seen with CT. Thus, the posterior fossa is more easily visualized on MRI than CT. Imaging is also performed without any ionizing radiation.


MRI is based on the magnetization properties of atomic nuclei. A powerful, uniform, external magnetic field is employed to align the protons that are normally randomly oriented within the water nuclei of the tissue being examined. This alignment (or magnetization) is next perturbed or disrupted by introduction of an external Radio Frequency (RF) energy. The nuclei return to their resting alignment through various relaxation processes and in so doing emit RF energy. After a certain period following the initial RF, the emitted signals are measured. Fourier transformation is used to convert the frequency information contained in the signal from each location in the imaged plane to corresponding intensity levels, which are then displayed as shades of gray in a matrix arrangement of pixels. By varying the sequence of RF pulses applied & collected, different types of images are created. Repetition Time (TR) is the amount of time between successive pulse sequences applied to the same slice. Time to Echo (TE) is the time between the delivery of the RF pulse and the receipt of the echo signal.

Tissue can be characterized by two different relaxation times T1 and T2. T1 (longitudinal relaxation time) is the time constant which determines the rate at which excited protons return to equilibrium. It is a measure of the time taken for spinning protons to realign with the external magnetic field. T2 (transverse relaxation time) is the time constant which determines the rate at which excited protons reach equilibrium or go out of phase with each other. It is a measure of the time taken for spinning protons to lose phase coherence among the nuclei spinning perpendicular to the main field.


The most common MRI sequences are T1-weighted and T2-weighted scans. T1-weighted images are produced by using short TE and TR times. The contrast and brightness of the image are predominately determined by T1 properties of tissue. Conversely, T2-weighted images are produced by using longer TE and TR times. In these images, the contrast and brightness are predominately determined by the T2 properties of tissue.

In general, T1- and T2-weighted images can be easily differentiated by looking the CSF. CSF is dark on T1-weighted imaging and bright on T2-weighted imaging.

A third commonly used sequence is the Fluid Attenuated Inversion Recovery (Flair). The Flair sequence is similar to a T2-weighted image except that the TE and TR times are very long. By doing so, abnormalities remain bright but normal CSF fluid is attenuated and made dark. This sequence is very sensitive to pathology and makes the differentiation between CSF and an abnormality much easier.

(short TR and TE)
500 14
(long TR and TE)
4000 90
(very long TR and TE
9000 114

Above: Most common MRI Sequences and their Approximate TR and TE times.

T1-weighted imaging can also be performed while infusing Gadolinium (Gad). Gad is a non-toxic paramagnetic contrast enhancement agent. When injected during the scan, Gad changes signal intensities by shortening T1. Thus, Gad is very bright on T1-weighted images. Gad enhanced images are especially useful in looking at vascular structures and breakdown in the blood-brain barrier [e.g., tumors, abscesses, inflammation (herpes simplex encephalitis, multiple sclerosis, etc.)].

Diffusion weighted imaging (DWI) is designed to detect the random movements of water protons. Water molecules diffuse relatively freely in the extracellular space; their movement is significantly restricted in the intracellular space. Spontaneous movements, referred to as diffusion, rapidly become restricted in ischemic brain tissue. During ischemia, the sodium - potassium pump shuts down and sodium accumulates intracellularly. Water then shifts from the extracellular to the intracellular space due to the osmotic gradient. As water movement becomes restricted intracellularly, this results in an extremely bright signal on DWI. Thus, DWI is an extremely sensitive method for detecting acute stroke.

Comparison of T1 vs. T2 vs. Flair (Brain)


T1-Weighted T2-Weighted Flair
CSF Dark Bright Dark
White Matter Light Dark Gray Dark Gray
Cortex Gray Light Gray Light Gray
Fat (within bone marrow) Bright Light Light

(infection, demyelination)

Dark Bright Bright

Comparison of T1 vs. T1 with Gadolinium


Note the Gad Enhanced Bright Signal in the Blood Vessels

Comparison of Flair vs. Diffusion-weighted

Note the Acute Infarction Only Seen on DWI

Comparison of T1 vs. T2 - Spine


T1-Weighted T2-Weighted
CSF Dark Bright
Muscle Gray Dark Gray
Spinal Cord Gray Light Gray
Fat (subcutaneous tissue) Bright Light
Disk (if intact and hydrated) Gray Bright
Air (pharynx) Very Dark Very Dark

(edema, infarction, demyelination)

Dark Bright


  Vascular (ischemic and hemorrhagic stroke, AVM, aneurysm, venous thrombosis)

  Tumor (primary CNS and metastatic)

  Infection (abscess, cerebritis, encephalitis, meningitis)

  Inflammatory/Demyelinating Lesions (multiple sclerosis, sarcoidosis, etc.)

  Trauma (epidural hematoma, subdural hematoma, contusion)


  Congenital Malformations


  Subject to motion artifact

  Inferior to CT in detecting acute hemorrhage

  Inferior to CT in detection of bony injury

  Requires prolonged acquisition time for many images


There are few contraindications to MRI. Most contraindications to MRI can be divided into the following groups:

●  Implanted devices and other metallic devices

- Pacemakers and other implanted electronic devices
- Aneurysm clips and other magnetizable materials
- Cochlear implants
- Some artificial heart valves

   Intraocular metallic foreign bodies

- Screening CT of the orbits if history suggests possible metallic foreign body in the eye

  Unstable patients (most resuscitation equipment cannot be brought into the scanning room)

  Pregnancy (relative contraindication due to unknown effects on the fetus)

  Other severe agitation, or claustrophobia (may require anesthesia assistance)

                 Revised 07/04/16
Copyrighted 2006, David C Preston, MD