MR Pulse Sequences

Objective

Physic overview Basic sequences Clinical Application

MRI
MRI:

Magnetic resonance imaging Excellent anatomic and pathologic detail Recent technologic advances

Commom symbols of pulse sequence diagrams

MRI The basis concept

T1 recovery T2 and T2* decay Repetition time: TR Echo time: TE Contrast weighting

Physics overview

(Net magnetization vector)

Magnetization relaxation and decay

Fat: Shorter T1 (recovers faster) Shorter T2 (decays faster) Water (long T1 and T2) T2* - depends on the magnetic enviroment (external field) - Decay of both fat and water occurs very quikly

Definitions: TR and TE
Two key parameters TR(ms) and TE(ms) are key to the creation of image contrast TR: The time between the application of an RF excitation pulse and the start of the next RF pulse TE: the time between the application of RF pulse and the peak of echo detected

MR Signal LocalizationGradients

Gradients are linear variations of the magnetic field strength in a selected region. Three types of Gradients are applied The section-selective gradient: The phase-encoding gradient: The frequency-encoding gradient

Imaging Plane

Slice selection

Encoding Phase Frequency

Coronal

Gy

Gx Gy

Gz Gx

Axial (body Gz imaging) Axial (head Gz imaging) Sagital Gx

Gx

Gy

Gy

Gz

It can compute the exact location and amplitude of the signal K- Space and the Image Matrix- > Fourrier: Image

Tissue Contrast

Tissue Contrast

Tissue Contrast

Tissue Contrast

Tissue contrast

T1
TR : 500ms. TE :15ms. AT: 4 min.

DP
TR : 2000ms. TE : 20ms

T2
TR : 2000ms. TE : 120ms. -AT : 4 min. 25 sec.

Effect of TR and TE on MR imaging contrast

Imaging technique T1 weighting T2 weighting TR Short Long TE Short Long Short

Proton-density Long weighting

Typical TR and TE values for SE and GRE

TR (ms) Sequence Short SE GRE Long TE (ms) Short Long >60 >10

250-700>2000 10-20 <50 >100 1-5

Basis Sequences
Spin-echo Gradient-echo Inversion-recovery Echo-planar

imaging MR angiographic

SE Sequences

Tissue contrast

T1: Anatomy T1 +Gd: Pathology T2 : Pathology Density proton WI: Both Anatomy and Pathology

Hypersignal on T1

Sub-acute Hematome: (MetHb). Fat. Artifacts. Post-hypophyse. Protein Melanine (metastase of melanoma). Manganse. calcifications.

The signal intensity of various tissue T1 SE

Air, mineral rich tissue (cortical bone, stones), fast flowing blood Collagenous tisue (ligament, tendons, scars) High free water tissue: Kidneys, liver, muscle... Proteinaceous tissue (abcess, complex cysts, sylnovial) Fat, blood products (metHb), slow-flowing blood, radiation change, contrast agent

The signal intensity of various tissue on T2 SE

Air, mineral rich tissue, fast-flowing blood Collagenous tissue, bone islands Hight bound water tissues (liver, pancreas, adrenals) Fat, fatty bone marrow

High free water tissue, proteinceous tissue, blood products

Advances in MR imaging technology have enabled a reduction in acquisition time with the use of Fast SE sequences

Fast SE

Echo train N: Echo train length

SE and Fast SE

7min 17s

Fast SE: 36s

Fast SE

Sequentially increasing the TE of a sequence weights it more heavily toward T2: MR cholangiopancreatography: Bile ducts and Pancreatic ducts MRI: Hemangiomas and Cysts

Fast SE: T2W (TE= 650)

Hemangiomas or Cysts Fast SE: T2W (TE= 83) Fast SE: T2W (TE= 180)

SE and Fast SE Sequences

GRE Sequences

RF pulse is applied that partly flips the NMV into the tranverse plane (variable flip angle). Gradients, as opposed to RF pulses, are used to dephase (negative gradient) and rephase (positive gradient) tranverse magnetization

GRE Sequence

Sensitive to magnetic susceptibility differences between tissues. T2*W: (TR : 800ms; TE : 15 ms), 3 min.

GRE Sequence
Hemorrhagic Pigmented villonodular synovitis Calcification T2* + Gd: Perfusion study Mapping of human brain function: Blood oxygenation level-dependent imaging: BOLD Deoxyhemoglobin in the vasculature -> Reflection of neuronal activity

GRE Sequence Pigmented villonodular synovitis

Coronal PD FSE, fat suppression

Coronal T2*-weighted GRE: Blooming artifact Hemosiderin

GRE Sequence Perfusion

GRE Sequence
Partially Refocused GRE: + MR angiography + Pathology of Internal auditory canal Fully Refocused GRE - All the gradients are refocused --> Signal improvement SSFP: Steady-state free precession: + Typical fast + Hight Signal-to-noise ratio + Useful for Cardiac imaging, High resolution of IAC : Spoiled GRE: T1 + Gd

Oblique sagital T2W SSFP

T1W Spoiled GRE

GRE Sequence Fully Refocused GRE CISS/ FIESTA

CISS: State steady interference construction - Hight resolution, 3D - Acquisition Time: 5min - Pathology: + Cranial nerve: Tumor, neuro-vascular conflict + Meningo-os fistula

T2 SE

CISS

CISS

TOF 3D

Common names for GRE Sequences Used by Major Vendors

Conventional Inversion Recovery

TI: The interval between the 180 pulse and the 90 pulse

Fluid is dark

Conventional Inversion Recovery

STIR: Short TI inversion-recovery FLAIR: Fluid attenuated inversionrecovery TIR (Turbo Inversion Recuperation)

Conventional Inversion Recovery STIR

Coronal STIR Fracture of the distal tibial
To null signal from the Fat : TI 140 msec

Bone marrow edema

Fast SE with spectral fat suppression

STIR TE 140-150 msec

FLAIR

To null signal from the Fluid

Technics TR : 8000 ms. TE : 105 ms. Acquisition time : 3 min Lung cancer

FLAIR Sequence
-Interest: very sensibility + White matter pathology (SEP, Inflammation, infection, tumor, vascular). + Epidermoid Kysts.
-

Disadvantage: No specific, artifarct of flow at the posterior fossa

TIR

(Turbo Inversion Recuperation)

-Advantage: Good contrast white/gray matter - Application: + Study hippocampe: (seizure) + Malformative Pathology (anormal of
neuronal migration, Gyration, Heterotopies)

Echo-Planar Imaging
A single echo train is used to collect data from all lines of k-space during one TR -> shortents the acquisition time 2 types of EPI: SE and GRE sequences Technique of choice for + Diffusion-weighted imaging: EPI SE sequence + Cerebral Perfusion Magnetic

EPI

EPI GRE

DWI
To distinguish between + Rapid diffusion of protons: unrestriction Diff. Principle: Eitherof protons: restriction Diff. + Slow diffusion GRE or Fast SE

+ Supplement Gradient to dephase:B0, B1000 (millitesla/mm2) + Gradient to rephase (equal gradient pulses applied on each side of the 180 RF pulse in EPS)

DW Stroke

Restriction Hight signal intensity

EPI -DW
No net movement:Rephase (-) Hight signal intensity Net movement: Rephase (+) Signal intensity decrease

Cytotoxique edema, abcess

Hyposignal: Fluid, LCR

DW and ADC
Cart ADC: Apparent diffusion coefficient For the calculation of ADC maps 2 sets of images + One obtained without application of a Diffusion gradient: T2WI or B0 + One obtained with a diffusion gradient

Cart ADC

Dark and white image : - ADC decrease dark, viscosite increase: + Recent infarction + Abcess + Recent hematome - ADC increase, white, mobile fluid: + LCR + Tumor kysts Color image: - ADC decrease = blue - ADC increase = red

DW and ADC Whats the purpose?

DW and ADC Ischemia ?

DW-ADC Ischemia
DWI

Cytotoxique Edema

DW-ADC Arachnoide and Epidermoide Kyst ?

DW-ADC Primary Tumors:Glioblastoma ?

DW-ADC Metastase ?

Metastase: Breast Cancer

DW-ADC Metastase ?

55 years old, man. Metastase bronchal epidermoid carcinome

DW-ADC Abces ?

Sensibility +++ Specific: +++

Rana and al. AJNR 2002

DW-ADC Abces

Different Diagnosis: Metastase: Carcinome epidermoid Radionecrosis Hemorrhage in tumor

MR Angiography
- Exploration of vessel: No invasive technique - Principle : Creation of contrast
Blood flow: hypersignal Suppression of stational tissue

- 4 Principle sequences:
+ TOF: Time Of Flight + MOTSA: Multiple onerlapping thin-slab acquisition + Contrast-enhanced MRA (Fast GRE 3D+Gd; FISP)

MRA TOF and MOTSA

Multiple RF pulses applied with shorts TRs saturate the spin in stationary tissues: Suppression of the signal from stationary tissues in the imaging slab 2D: section-by-section 3D: larger volume MOTSA: Hybrid result of 2D and 3D the Thinner slab -> the Less deleteriously affected by distal

TOF

GRE: Shorts TR: 40-50msec

Exploration of circulate Flow: Artery or Vein

TOF
- 2D :
- Many Acquisitions by continuous coups (Section-by Section) - Favorage: + Slow flow: Veins, before of severe stenosis. + Exam for large zone Exam the Volume on only times The volumes acquisition limited 5-10cm. - Precise the anatomy better than 2D. - Saturate the slow flow. Exam the artery Reconstruction all of the plan: MIP Acquisition time: 7
-

- 3D :

Original Coup: TOF

MIP Reconstructions

Exam the veins (Dural sinus). Interest: Thrombophlebite Bilan extension the veins of Meningioma

Polygone TOF
Exam the arteries intra-cranial: polygone of Willis - Vascular Malformations:Ane., MAV - Bilan extension vessel of tumor - Nervo-vascular conflict (Original coups)

Original Coups

MIP Reconstructions

MRA Contrast-enhanced MR angiography

T1+ Gd: Shorten the T1 of Blood -> Hight signal intensity on T1WI Fast GRE, 3D (Short Acquisition times:44sec) Interest: Exploration of cervical vessels from their origins to cranial base.

Original Coups

MIP Reconstructions

MRA

Contrast MRA

MIP on Contrast MRA

ARM by Phase of Contrast

- To dephase of mobile protons, using two inverse pole gradients: + Immobile Protons, dephase and rephage: No signal + Mobile Protons : signal - The different levels of phase depend on the velocity of circulated proton Necessary to select the encode of potential speed to analyze the vessel

MRA by Phase of Contrast

MRA Phase-contrast Imaging

Providing information about the phase (direction) and the velocity (magnitude) of flow 2D and 3D Hight signal: Flow moves from RT->LT Sup-> Inf Ant-> Pos No signal: Flow moves from:

Phase-contrast Subclavian steal

Fat-related Imaging Techniques

Fat Signal Suppression: 3 ways + RF- uncoherent gradient: MRI +Gd + Inversion-recovery pulse: STIR + Water-excitation technique: Spectral-spatial RF pulse

Fat-related Imaging Techniques

T1 fat suppression

Water excitation fat suppression

STIR

Fat-saturated T1WI

Interest - To confirm the fat in the lesion. - Bilan lesions extension to the vessel and the space containing fat: - Arterial dissection

Lipome

Original 3D TOF.

Fat-saturated T1W images.

In-phase and Out-of-Phase Imaging

Different chemical environments of 1H in fat ( CH2) and water (H2O) Spoiled GRE: Fat and Water In-phase: TE =4,2-4,5 msec (1.5 T) Out of phase: TE = 2,1-2,3 msec To depict microscopic fat: Adrenal adenomas # Adrenal carcinomas Steatosis Fat + -> null on out of phase

In-phase and Out-of-Phase Imaging

T1 W Spoiled GRE: In-phase: TE= 4.2

T1 W Spoiled GRE: Out of phase: TE= 2.1

Adrenal adenoma

T1

T2

T1 Fat sat

T1

T1 +Gd T2

MR Spectroscopy

MR Spectroscopy

MRS provides a measure of Brain chemistry: Each metabolite appears at a specific ppm, and each one reflects specific cellular and biochemical processes Biochemical changes in Tumors, Stroke, Epilepsy, Metabolic disorders, Infections and Neurodegenerative diseases Interpretation: MRI and MRS

1H, 23Na; 31P: (1H higher signal-to-noise)

(ppm: Parts per millions)

Observable Proton Metabolites

ppm
0.9-1.4 1.3 2.0 2.2-2.4 3.0 3.2 3.5 1.2 1.48 3.4&3.8 3.8

Metabolite
Lipids Lactate NAA Glutamine/GABA Creatine Choline myo-inositol Ethanol Alanine Glucose Mannitol

Properties
Products of brain destruction Product of anaerobic glycolysis Neuronal marker Neurotransmitters Energy metabolism Cell membrane marker Glial cell marker, osmolyte hormone receptor mechanisms Triplet Present in meningiomas Increased in diabetes Rx for increased ICP

NAA: Decreases with any disease that adversely affects neuronal integ-rity Creatine provides a measure of energy stores Choline: measure of increased cellular turnover Elevate in tumors, Inflammatory processes Myoinositol: located primarily in astrocytes

Increased in hypernatremia, in tubers and Alzeimer D.

Basis physical Principles

The resonant frequencies of Protons: 10MHz at 0.3 T 300MHz at 7 T 63-64 MHZ at 1.5 T Higher field strength, Higher signal-tonoise and better separation of the metabolite peaks

Study the biochemical structure of the disovle molecule in the water Aanalyze the character of chemical movement of the molecules after suppression the signal of water by supplemental magnetique field

Water and Fat is suppressed by: Technics: CHESS (CHEmical-Shift Selective) IR (Inversion Recorvery) STEAM or PRESS pulse sequence (Stimulated Echo Acquisition Mode): Refocuses 90 (Point Resolved SpectroScopy): Refocuses 180 CSI (Chemical Shift Imaging) refers to multi-voxel MRS SI (Spectroscopic Imaging) displays the data depending on the concentration of a particular metabolite

PRESS (point resolved spectroscopy) Double spin-echo technique Subject to T2 loss

STEAM (stimulated echo acquisition mode):

Can use shorter TE, allow to see more metabolites such as myoinositol Less SNR than PRESS

SETTING UP MR SPECTROSCOPY
Choose the right sequence + Homogeneous lesion: single voxel + Heterogeneous lesion (ring-enhancing, edema): multivoxel Choose the volume (4-8 cm3) Avoid skull, sinus, fat, blood products, vasogenic edema, water, foreign bodies and radioactive seeds

Short TE of 30msec: Metabolites with both short and long T2 relaxation times are observed: Long TE of 270 msec, only metabolites with a long T2 are seen: NAA, Creatinin and Choline TE of 144 msec: Lactate at 1.3 ppm

Normal MR Spectrum

2 GM

Hunters angle

1 2 1 WM

Hunters Angle:

NAA/Cr, NAA/Cho, and Cho/Cr Normal NAA/Cr NAA/Cho Cho/Cr 2.0 1.6 1.2 Abnormal < 1.6 < 1.2 > 1.5

Metabolite Ratios

Malignancy increases: NAA and Creatine decrease + Displaces or destroys neurons + Very malignancy: Hight metabolic activity and deplete the energy stores -> Reduce Creatine Choline, Lactate and Lipid increase + Very hypercellular tumors with rapid growth elevate the Cholin levels + Lipid: in necrotic portions of tumors + Lactats appears when tumors out grow their blood supply and start ultilizing anaerobic glycosis

MRS Brain Tumors: Degree of Malignancy

MRS Gliomblastoma

Elevation of Cho and Decrease NAA Lactat doublet

Glial tumor or Non-glial tumors

Gliomas: Elevation of Cholin beyond the margin of enhancement High grade astrocytoma # metastasis: the presence of high choline in the peritumoral region. Non glial tumors: Have little or no NAA Meningoma: Elevation of Alanine at 1.48ppm: PNET or medulloblastomas have higher elevations of Choline than astrocytoma Lymphomas have higher elevated lipids compared to GBM. Craniopharyngiomas have a peak in the lactate-lipid range.

Tumor recurrence after Radi or Sur.

Elevated cholin is a marker for recurrent tumor Radiation change generally exhibits low NAA, Creatine and Cholin on Spectroscopy If radiation necrosis is present, the spectrum may reveal elevated lipids and lactate

TUMOR VS RADIATION NECROSIS

Radiation necrosis have high lactate and lipids (which may be also found after radiotherapy)

MRS Ischemia and Infection

Ischemia + Anaerobic glycosis and lactate accumulates -> Hight Lactate + Infarction: Lipid increase Brain abcesses destroy or displace brain tissue + NAA: not present + Bacterial abcesses: Lactate, cytosolic acid, alanine and Acetate + Toxoplasmosis and Tuberculomas: Prominent peaks from Lactate and Lipids

Infections Diseases
Brain abcesses destroy or displace brain tissue NAA: not present Bacterial abcesses: Lactate, cytosolic acid, alanine and Acetate Toxoplasmosis and Tuberculomas: Prominent peaks from Lactate and Lipids

Metabolic Pathology
Pediatric Metabolic Brain Disorders (MRS)
Maple syrup urine disease: elevated branched chain amino acids(0.9-1.0ppm) Diabetic ketoacidosis: elevated acetone(2.2ppm) & glucose(3.4ppm) Galactosemia: galactitol detected(3.67-3.74ppm) Phenylketonuria: phenylalanine detected(7.3ppm) Lipid storage diseases (Niemann-Pick): elevated lipids(0.7-1.6ppm)

Pediatric Metabolic Brain Disorders (MRS)

Canavans disease

Markedly increased NAA Mitochondrial disorders Markedly increased lactate

Leighs, MERRF, MELAS

Peroxisomal disorders
Increased sI @ 3.35 (syllo-inositol)

How about protocols MRI for each disease ?

Thank you for your attentions!

Protocol dIRM dans exploration encphale

Standard: T1 sagital T2 axial Flaire axial Comitialit : T1 sag-T1 Stir Coronal T2* axial Flaire coronal +/- T1 axial ou coronal avec Gd

Protocol dIRM dans exploration encphale

Dmence: T1 sag-T1 Stir coronal (hippo) Flaire axial T1 axial Gd Hypophyse: T1 sag et coronal T1 sag et coronal avec Gd T2 coronal ARM post Embolisation: T2 axial TOF

Surdit rtrocochlaires, Vertiges T1 sag T2 axial coupes fines encphales CISS 3D axial T1 axial FS pre et post Gd +/-Coro Controle Neurinome de lacoustique non opr T1 Gd axial et coro : Volume T2 axial Controle Neurinome opr T1 pre et post Gd FS T2 axial

Protocol dIRM dans exploration encphale

Protocol dIRM dans exploration encphale

Orbites: T1 PNO T2 PNO T2 coro Stir +/-T1 avec Gd FS Conflit Vasculo-nerveux T1 sag T2 axial coupes fines encphales CISS 3D axial TOF Polygone

Artifact

Schemical shift Artifact