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Basic Principles of MR

In order to perform MRI, we first need a strong magnetic field. The field strength of the magnets used for MR is measured in units of Tesla. One (1) Tesla is equal to 10,000 Gauss. The magnetic field of the earth is approximately 0.5 Gauss. Given that relationship, a 1.0 T magnet has a magnetic field approximately 20,000 times stronger than that of the earth. The type of magnets used for MR imaging usually belongs to one of three types; permanent, resistive, and superconductive. Superconducting magnets are the most common system used in MRI technology. They are made from coils of wire (as are resistive magnets) and thus produce a horizontal field. They use liquid helium to keep the magnet wire at 4 degrees Kelvin where there is no resistance (electron moves freely). Magnetic Properties of Matter Magnetism is a fundamental property of matter. The three types of magnetic properties are: diamagnetic, paramagnetic, and ferromagnetic. These three properties are illustrated in figure 3.

Atomic Structure The nucleus of an atom consists of two particles; protons and neutrons. The protons have a positive charge and the neutrons have a neutral charge. The atomic number represents the number of protons in the nucleus. The atomic mass number is the total number of protons and neutrons. Orbiting the nucleus are the electrons, which carry a negative charge (figure 5). All of these particles are in motion. Both the neutrons and protons spin about their axis. The electrons, in addition to orbiting the nucleus, also

spin about their axis. The spinning of the nuclear particles produces angular momentum. If an atom has an even number of both protons and
n clinical practice, MRI is used to distinguish pathologic tissue (such as a brain tumor) from normal tissue. One advantage of an MRI scan is that it is harmless to the patient. It uses strong magnetic fields and nonionizing radiation in the radio frequency range, unlike CT scans andtraditional X-rays, which both use ionizing radiation. While CT provides good spatial resolution (the ability to distinguish two separate structures an arbitrarily small distance from each other), MRI provides comparable resolution with far better contrast resolution (the ability to distinguish the differences between two arbitrarily similar but not identical tissues). The basis of this ability is the complex library of pulse sequences that the modern medical MRI scanner includes, each of which is optimized to provide image contrast based on the chemical sensitivity of MRI.

Effects of TR and TE on MR signal.

For example, with particular values of the echo time (TE) and the repetition time (TR), which are basic parameters of image acquisition, a sequence takes on the property of T2-weighting. On a T2-weighted scan, water- and fluid-containing tissues are bright (most modern T2 sequences are actually fast T2 sequences) and fat-containing tissues are dark. The reverse is true for T1-weighted images. Damaged tissue tends to develop edema, which makes a T2-weighted sequence sensitive for pathology, and generally able to distinguish pathologic tissue from normal tissue. With the addition of an additional radio frequency pulse and additional manipulation of the magnetic gradients, a T2-weighted sequence can be converted to a FLAIR sequence, in which free water is now dark, but edematous tissues remain bright. This sequence in particular is currently the most sensitive way to evaluate the brain for demyelinating diseases, such as multiple sclerosis. The typical MRI examination consists of 520 sequences, each of which are chosen to provide a particular type of information about the subject tissues. This information is then synthesized by the interpreting physician.


MRI scans

[edit]T1-weighted MRI Main article: Spin-lattice relaxation time T1-weighted scans are a standard basic scan, in particular differentiating fat from water - with water darker and fat brighter[24] use a gradient echo (GRE) sequence, with short TE and short TR. This is one of the basic types of MR contrast and is a commonly run clinical scan. The T1weighting can be increased (improving contrast) with the use of an inversion pulse as in an MP-RAGE sequence. Due to the short repetition time (TR) this scan can be run very fast allowing the collection of high resolution 3D datasets. A T1 reducing gadolinium contrast agent is also commonly used, with a T1 scan being collected before and after administration of contrast agent to compare the difference. In the brain T1-weighted scans provide good gray matter/white matter contrast; in other words, T1-weighted images highlight fat deposition. [edit]T2-weighted MRI Main article: Spin-spin relaxation time T2-weighted scans are another basic type. Like the T1-weighted scan, fat is differentiated from water - but in this case fat shows darker, and water lighter. For example, in the case of cerebral and spinal study, the CSF (cerebrospinal fluid) will be lighter in T2-weighted images. These scans are therefore particularly well suited to imaging edema, with long TE and long TR. Because the spin echo sequence is less susceptible to inhomogeneities in the magnetic field, these images have long been a clinical workhorse. [edit]T* 2-weighted MRI T* 2 (pronounced "T 2 star") weighted scans use a gradient echo (GRE) sequence, with long TE and long TR. The gradient echo sequence used does not have the extra refocusing pulse used in spin echo so it is subject to additional losses above the normal T2 decay (referred to as T2), these taken together are called T* 2. This also makes it more prone to susceptibility losses at air/tissue boundaries, but can increase contrast for certain types of tissue, such as venous blood. [edit]Spin density weighted MRI Spin density, also called proton density, weighted scans try to have no contrast from either T2 or T1 decay, the only signal change coming from differences in the amount of available spins (hydrogen nuclei in water). It uses a spin echo or sometimes a gradient echo sequence, with short TE and long TR

Fluid attenuated inversion recovery (FLAIR)

Main article: Fluid attenuated inversion recovery Fluid Attenuated Inversion Recovery (FLAIR)[28] is an inversion-recovery pulse sequence used to null signal from fluids. For example, it can be used in brain imaging to suppress cerebrospinal fluid (CSF) so as to bring out the periventricular hyperintense lesions, such as multiple sclerosis (MS) plaques. By carefully choosing the inversion time TI (the time between the inversion and excitation pulses), the signal from any particular tissue can be suppressed.

MRI versus CT

A computed tomography (CT) scanner uses X-rays, a type of ionizing radiation, to acquire images, making it a good tool for examining tissue composed of elements of a higher atomic number than the tissue surrounding them, such as bone and calcifications (calcium based) within the body (carbon based flesh), or of structures (vessels, bowel). MRI, on the other hand, uses non-ionizing radio frequency (RF) signals to acquire its images and is best suited for soft tissue (although MRI can also be used to acquire images of bones, teeth[44] and even fossils[45]). In contrast, CT images are generated purely by X-ray attenuation, while a variety of properties may be used to generate contrast in MR images. By variation of scanning parameters, tissue contrast can be altered to enhance different features in an image (see Applications for more details). Both CT and MR images may be enhanced by the use of contrast agents. Contrast agents for CT contain elements of a high atomic number, relative to tissue, such as iodine or barium, while contrast agents for MRI have paramagnetic properties, such as gadoliniumand manganese, used to alter tissue relaxation times. CT and MRI scanners are able to generate multiple two-dimensional cross-sections (tomographs, or "slices") of tissue and three-dimensional reconstructions. MRI can generate cross-sectional images in any plane (including oblique planes). In the past, CT was limited to acquiring images in the axial (or near axial) plane. The scans used to be called Computed Axial Tomography scans (CAT scans). However, the development of multi-detector CT scanners with near-isotropic resolution, allows the CT scanner to produce data that can be retrospectively reconstructed in any plane with minimal loss of image quality. For purposes of tumor detection and identification in the brain, MRI is generally superior.[46][47] However, in the case of solid tumors of the abdomen and chest, CT is often preferred as it suffers less from motion artifacts. Furthermore, CT usually is more widely available, faster, and less expensive. However, CT has the disadvantage of exposing the patient to harmful ionizing radiation. MRI is also best suited for cases when a patient is to undergo the exam several times successively in the short term, because, unlike CT, it does not expose the patient to the hazards of ionizing radiation.

Hydrogen Atoms and Magnetic Moments


The steps of an MRI When patients slide into an MRI machine, they take with them the billions of atoms that make up the human body. For the purposes of an MRI scan, we're only concerned with the hydrogen atom, which is abundant since the body is mostly made up of water andfat. These atoms are randomly spinning, or precessing, on their axis, like a child's top. All of the atoms are going in various directions, but when placed in a magnetic field, the atoms line up in the direction of the field. These hydrogen atoms have a strong magnetic moment, which means that in a magnetic field, they line up in the direction of the field. Since the magnetic field runs straight down the center of the machine, the hydrogen protons line up so that they're pointing to either the patient's feet or the head. About half go each way, so that the vast majority of the protons cancel each other out -- that is, for each atom lined up toward the feet, one is lined up toward the head. Only a couple of protons out of every million aren't canceled out. This doesn't sound like much, but the sheer number of hydrogen atoms in the body is enough to create extremely detailed images. It's these unmatched atoms that we're concerned with now.

What Else Is Going on in an MRI Scan?

Next, the MRI machine applies a radio frequency (RF) pulse that is specific only to hydrogen. The system directs the pulse toward the area of the body we want to examine. When the pulse is applied, the unmatched protons absorb the energy and spin again in a different direction. This is the "resonance" part of MRI. The RF pulse forces them to spin at a particular frequency, in a particular direction. The specific frequency of resonance is called theLarmour frequency and is calculated based on the particular tissue being imaged and the strength of the main magnetic field. At approximately the same time, the three gradient magnets jump into the act. They are arranged in such a manner inside the main magnet that when they're turned on and off rapidly in a specific manner, they alter the main magnetic field on a local level. What this means is that we can pick exactly which area we want a picture of; this area is

referred to as the "slice." Think of a loaf of bread with slices as thin as a few millimeters -- the slices in MRI are that precise. Slices can be taken of any part of the body in any direction, giving doctors a huge advantage over any other imaging modality. That also means that you don't have to move for the machine to get an image from a different direction -- the machine can manipulate everything with the gradient magnets. But the machine makes a tremendous amount of noise during a scan, which sounds like a continual rapid hammering. That's due to the rising electrical current in the wires of the gradient magnets being opposed by the main magnetic field. The stronger the main field, the louder the gradient noise. In most MRI centers, you can bring a music player to drown out the racket, and patients are given earplugs. When the RF pulse is turned off, the hydrogen protons slowly return to their natural alignment within the magnetic field and release the energy absorbed from the RF pulses. When they do this, they give off a signal that the coils pick up and send to the computer system. But how is this signal converted into a picture that means anything?

HEAD IMAGING - MRI Protocol Overview

General Preparation
Use the Head coil with a sheet on the table, and a paper disposable towel for the coil sponge. Besides standard room exclusions, remove dentures, hair clips, hair combs, earrings, nose rings, necklaces. Remove upper body clothing with metallic trim i.e. studs, neck zippers, epaulette buttons, appliqu or embroidery or any clothes likely to create static electricity i.e. mohair, nylon. The patient must be given disposable earplugs to attenuate the gradient switching noise, unless either of these add significantly to claustrophobia. Position the patient so their head and neck are relaxed, but without rotation in either plane. The patient should be well supported to minimize movement. Pillows under the knees can help to decrease strain on the knees and lumbar lordosis, and also stabilize motion of the lower body. Excessive attempts at immobilization rarely work, but the comfort kit may stabilize involuntary movements

Centre the field of view on the Nasion in the midline, making minor adjustments for baseline tilt. Protocols have been developed to deal with a range of typical requests and presentations, but always review the images as they are collected and modify the examination as appropriate. Optional sequences are suggestions for better defining the lesions, and may be undertaken at the Radiographers' discretion or suggestion, or at the request of the Radiologist. When time permits, and where the patient is not distressed, experiment with these and other likely sequence options. Then share your experience with the other MRI radiographers to help develop better protocols. Never Override the SAR limits on the Head Coil of the VISION. blow. The fuse will


Used for general examination of the brain with no specific neurological symptoms. The technique should be modified with additional views or more topical slices if an unexpected lesion is discovered.

Optional Sequences

Sequences stored under Head/Standard_Brain_Exam SCOUT 3 plane GRE localisers PD + T2 AXIAL Turbo spin echo (TSE) axials. 5 mm thick with 50% gap Position slices parallel to the line joining the Genu and Splenium of the Corpus Callosum. Cover the brain from below the Foramen Magnum to the Vertex. Sat band just below inferior slice and parallel to the slices FLAIR AXIAL 5 mm slices 0.9 mm resolution FOV 230 mm T1 CORONAL Spin Echo coronals 5 mm thick with 50% gap Position perpendicular to the line joining the Genu and Splenium of the Corpus Callosum. T1_Coronal_low-susceptibilty Use this sequence when the patient has metal in the FOV as the standard T1 uses a very low bandwidth. MP-RAGE isotropic T1 Use this if there are multiple lesions, when you need 2 T1 views, or when needing a slice thickness less than 4 mm. Reconstruct images as required. Consider contrast for suspected intracranial tumours, where a known tumour has changed size. Post contrast, Scan 5 minutes after contrast. Use the MP-RAGE for most lesions except ? Lymphoma or in where there is a solitary metastases. In those cases use the SE sequence with a short TR and MTC



Intended to provide a detailed examination of the seventh and eight cranial nerves and the other C-P angle structures, especially for detecting acoustic neuromas. The fifth cranial nerve is included on imaging. General brain images are obtained to make the exam more comprehensive.

Typical Indications

? acoustic neuroma ? CP angle lesion SN deafness Vertigo or Tinnitus

Sequences stored under Head/ CP_ANGLE SCOUT Three plane low resolution scout PD + T2 AXIAL Full brain coverage TSE axials. 5 mm thick with 50% gap

Position slices parallel to the line joining the Genu and Splenium of the Corpus Callosum. Cover the brain from below the Foramen Magnum to the Vertex. Sat band just below inferior slice and parallel to the slices
CISS_Axial High resolution 3D bright fluid sequence to define the cochlea and semi-circular canals and outline the cranial nerves.

Centre on the Acoustic nerves, angle to place scan plane roughly parallel to the roof of
the 4th ventricle.

Use MPR software to correct positional errors and display full length of the nerves. See
the protocol notes describing how to create & film CISS or MP-RAGE MPRs for Acoustic Nerves

Variations & Optional Sequences

If the CISS images show an acoustic neuroma, or look suspicious do the isotropic MPRAGE and make axial MPRs. For follow up of known acoustics, and lesions treated with radiosurgery just do post contrast isotropic MP-RAGE with axial and coronal reconstructions.


Intended to detect sellar or parasellar lesions, to delineate intrusion into surrounding structures (optic chiasm, cavernous sinus, sphenoid sinus, frontal and temporal lobes, anterior brainstem, and to display any nasal cavity abnormality which may complicate a trans-sphenoidal surgical approach.

Typical Indications

Hormonal disturbances - Amenorhea, Hyperprolactinaemia, Acromegaly Query or known microadenoma (<10 mm) or macroadenoma (> 10 mm) Pituitary apoplexy (bleeding in pituitary) Sudden visual loss

Sequences stored under Head / Pituitary SCOUT Three plane low resolution scouts T2_CORONAL TurboSE T2 coronals positioned through the sella or lesion.

Place the rear slice through the Basilar artery.

Isotropic_MPRAGE Used for multi-planar reformatting.

Optional Sequences
PD+T2_BRAIN Sequence copied form the Standard brain examination for a general overview of the brain in patients with a non specific indication for Pituitary MRI T2_SAGITTAL For enhanced display of cystic lesions if they are not clearly visible on the MP RAGE images

Multi-planar Reconstructions
For more detailed instructions see "Creating & Filming MPRs for Pituitary Examinations"

Create 12 sagittal and 12 coronal T1 weighted images. Slice Thickness 1 or 2 mm for micro-adenomas, 3 mm or 4 mm for macro-adenomas. Use Double Oblique prescription on an axial work image to ensure that the planes are anatomically true. Define the sagittal locations from the right to the left, and the coronals from posterior to anterior to ensure easy filming in the proper direction.

Dynamic Contrast Pituitary Typical Indications

To identify small (>3mm) secreting pituitary adenomas so that a partial resection of the pituitary may be used rather than total.

Cushings Disease with asymmetric results in petrosal venous sampling, or other cases after discussion with Dr Taylor.

Sequences stored under Head /Pituitary

Preparation & Kit

20G Jelco 10 ml Saline Minimum volume extension tube Tape and tourniquet 2 x 10 ml syringes

Set up the jelco with the extension tube filled with saline. The contrast is injected rapidly (2 ml/sec) at the beginning of the second scan, and followed by a saline flush of 5-10 mls.

Contrast Doses (Half dose)

40 kg 50 kg 60 kg 70 kg 4 mls 5 mls 6 mls 7 mls 80 kg 90 kg 100 kg 110 kg 8 mls 9 mls 10 mls 11 mls

Perform a standard pituitary exam first unless done recently.


This is a series of TSE T1 coronal images intended to be used with a fast injection of half dose contrast. The injection is rapidly given at the start of the 2nd measurement. There is a 10 second pause between the first (precontrast) scan and the start of the continuous string of post contrast measurements to prepare the injector and give a countdown.

Filming and Analysis.

Low SNR means that lesions are hard to distinguish reliably by visual comparison. Images for a single patient must be presented consistently and filmed with the same window settings. Time curve graphs of the enhancement are produced to be able to objectively identify lesions.

Use Evaluate Dynamic Analysis to subtract each of the post contrast sequences from the precontrast mask. Film on 12 format Identify the slice locations within that cover the pituitary gland (usually 3 but can be 6) Magnify image to present a 53 mm FOV (magnify x 3) Film the normal views and the subtracted views as shown below, using 2 sheets for each if more than 3 locations include the gland. Use the same window settings for each image and for each series. The right levels are determined in the 3rd post contrast image.

Location 1 Pre contrast

Location 2

Location 3

36 sec post (normal image or subtraction)

1:48 post (normal image or subtraction)

3 min post (normal image or subtraction)


Intended to detect M.S. plaques in the white matter anywhere in the brain. Typical Indications MS Demyelanation Nystagmus (especially in young patient) Optic Neuritis

Sequences stored under Head / Demyelination SCOUT 3 plane GRE localisers Double_Echo_AXIAL Turbo spin echo (TSE) axials. 5 mm thick with 50% gap

Position slices parallel to the line joining the Genu and Splenium of the Corpus Callosum. Cover the brain from below the Foramen Magnum to the Vertex. Sat band just below inferior slice and parallel to the slices
Sagittal_FLAIR 5 mm slices 0.9 mm resolution FOV 230 mm

Position parallel to the corpus callosum

T1 CORONAL Spin Echo coronals 5 mm thick with 40% gap

Position perpendicular to the line joining the Genu and Splenium of the Corpus Callosum.


Intended to detect temporal lobe lesions which are likely to be the root course of complex partial seizures which have not responded to medication. The films may provide planning information for partial or full temporal lobectomy. Lesions could include tumour, scar, infarct, miscellaneous gliotic change or mesial temporal sclerosis. The examination must also screen for other lesions in the brain.

Typical Indications
Temporal lobe epilepsy (TLE) Complex partial seizures (CPS) Mesial temporal sclerosis (MTS) Short term memory loss (STM) Partial seizures Temporal focus on EEG

Orthodontic Braces These are common in young TLE patients and will create substantial artefact even in axial views of the temporal lobes. Use the low susceptibility T1 sequence. You may need to repeat the sequence with half the acquisitions, 100% phase oversampling, and the phase running S-I to shift braces artefact from the temporal lobes as the standard T1 uses a very low bandwidth. Sequences stored under Head / Temporal_Lobe Scout 3 plane GRE localisers Sagittal Scout 3 sagittal FLASH images to help identify the line of the hippocampal grey matter. PD + T2 AXIAL Turbo spin echo (TSE) axials. 5 mm thick with 50% gap

Position slices parallel to the line joining the Genu and Splenium of the Corpus Callosum. Cover the brain from below the Foramen Magnum to the Vertex. Sat band just below inferior slice and parallel to the slices
T1 Isotropic MP-Rage (sagittal acquisition)

Run and create MPRs in the coronal and axial planes relative to the Hippocampus (see
below) T2 TSE Coronal 3 mm slices 0.65mm resolution

Position perpendicular to the line of the Hippocampal grey matter, cover form the
anterior temporal horn to the abutment of the Hippocampus and the corpus callosum

FLAIR Coronal 5 mm slices 0.9 mm resolution FOV 230 mm

Position perpendicular to the line of the Hippocampal grey matter, cover form the
anterior temporal horn to the abutment of the Hippocampus and the corpus callosum

Optional Sequences
True IR Coronals

Position perpendicular to the line of the Hippocampal grey matter, cover form the
anterior temporal horn to the abutment of the Hippocampus and the corpus callosum True IR Axials

Position parallel to the line of the Hippocampal grey matter.