BIOE 220/RAD 220 REVIEW SESSIONJanuary 23, 2011

Your TAs• Physics TA: Michael Marx, mikemarx@stanford.edu• Anatomy TA: Shubhra Jain, jainshubhr@gmail.com

• We will have weekly review sessions, Mondays at 5:30 in the Lucas Learning Center. We will review the material from the previous lectures and then have time for questions and homework help.

• Please feel free to email us with any questions. We will reply within 24 hours to email, and can make time for additional meetings outside of the review sessions if there’s demand.

• If you would like us to cover something specific at the weekly review session, please email us both by Sunday night.

Today’s Schedule1. Course Overview – Setting expectations2. Basics of MRI, MRI Review3. Imaging Conventions4. Neuro-Anatomy Review5. Time For Questions

Course Overview - Outline• Jan 9 – Introduction, MR Signal, CNS Overview• Jan 11 – MR Relaxation, Brain Anatomy 1(Lobes, Gyri, Sulci)• Jan 18 – Radiography, DSA, CT• Jan 23 – Contrast Agents, MR Gradients, DWI, 1D Localization, Brain Anatomy 2 (Deeper Structures,

Cerebellum, Pituitary)• Jan 25 – MRA, Orbits, Brain Coverings, Neurovascular Anatomy• Jan 30 – MR Slice Selection, Sampling, SNR• Feb 1 – Ultrasound• Feb 6 – Brain Development• Feb 8 – MR Image Formation• Feb 13 – Rendering Lab• Feb 15 – Midterm• Feb 22 – US Doppler, Carotid Anatomy, US Lab• Feb 27 – Spine and Spinal Cord• Feb 29 – MR Pulse Sequences, Angiography, Quantitative Flow Applications• Mar 5 – Perfusion Imaging, Cranial Nerves• Mar 7 – fMRI, Oxygenation, Brain Autoregulation in Health and Disease• Mar 12 – MR Lab• Mar 14 – DTI, Functional Neuroanatomy & Review• Mar 23 – Friday – 8:30 Final Exam

Course Overview - Expectations• The course is split about 50/50 between physics and anatomy

when it comes to class time, homework problems, and exam questions• Engineering students are often stronger with the physics and weaker with

anatomy• Science or medical students are often the reverse• Differences in student backgrounds should mostly balance out, so don’t

worry too much about it• The first physics lectures (MRI intro) are about as difficult as they

get this quarter, so don’t extrapolate difficulty and get worried• Movies on the web site should help with MRI intuition

• For anatomy, repetition is key to memorization. Make sure to review the slides, videos, and other resources• You will be given a list of terms that you’re responsible for on an exam, so

you don’t need to memorize spelling

Basics of MRI – B0

• MRI measures oscillating magnetic fields created by spinning water protons

• A large magnetic field B0 is applied in the ẑ direction• This magnetic field is always on, created by a superconducting

electromagnet (cooled by liquid helium)• The ẑ direction points through the magnet, which will generally be

P/I direction

• Left at rest, net magnetization M0 will align in the ẑ direction• We can’t measure magnetization in the same direction as B0, so it’s

necessary to rotate the magnetization into the transverse (xy) plane to measure it

Basics of MRI – Precession Frequency

• Protons rotate at a frequency determined by the gyromagnetic ratio• 𝑓0 Larmor frequency = γB≣ 0

• γ = 42.58 MHz/T for water hydrogen• Typical clinical scanners will be 1.5T or 3.0T

• In “lab frame,” our coordinate system is stationary, so the spins rotate at the Larmor frequency

• In “rotating frame,” the coordinate system rotates about ẑ at the Larmor frequency, so spins (magnetization) appear stationary

Basics of MRI – RF Pulses• To measure M0, it must be tipped into xy plane• In rotating frame, we can apply a magnetic field B1 to

apply a torque to M• Rotation due to B1 can be calculated using Larmor frequency• τ = M x B, so you can figure out direction of rotation using right

hand rule (point fingers towards M, curl them towards B, your thumb points in the direction of the torque)

Basics of MRI – Relaxation• Protons that aren’t perfectly on-resonance (rotating at

expected Larmor frequency) will rotate in rotating frame• Magnetization in the transverse plane decays quickly due to

dephasing• Fast dephasing is T2

’ decay, which contributes to T2*• This is imaged with GRE – Gradient Recalled Echoes

• Transverse magnetization can be refocused with a 180 degree pulse, which refocuses some of the off resonance• Refocused intensity decays with T2

• This is imaged with SE – Spin Echoes• As long as the spins are in the presence of B0, T1 recovery will

be occurring• Magnetization in the ẑ direction will be recovering towards M0

Basics of MRI – Relaxation Coefficients

• Different tissues in the body will have different T1 and T2 coefficients• These differences are what provide contrast in MRI images

• Images can be given different weighting (contribution from T1, T2, and M0) based on the pulse sequence timings

• Materials with a longer T2 tend to have longer T1

• Stationary fluid has very long recover times, so it will appear very bright in T2 weighting and dark in T1 weighting… easiest way to figure out weighting

• You should memorize this equation, and understand it well enough to re-derive it: •

MRI Basics – Contrast Summary

Imaging Conventions

Axial Plane ( CT, MR)

CT v/s MRI• If cortical bone is bright, it’s CT.• If cortical bone is dark, it’s MRI.• If fat is bright, it’s MRI.• Fat can be dark or bright on MRI.

• Hints: MRI is really good for looking at the musculature. Abdominal imagers really like CT.

CT Knee

Cortical bone is brightFat is dark

Proton Density-Weighted MRI Knee

Fat is bright. Cortical boneis dark, fluid is bright

X-ray CT, US, PET, or MRI??

X-ray CT, US, PET, or MRI??

X-RAY, CT, US, PET, OR MRI??

X-ray CT, US, PET, or MRI??

X-ray CT, US, PET, or MRI??

Overview of the nervous system• Central nervous System

• Brain• Spinal Cord• Cranial Nerves

• Peripheral Nervous System• Peripheral Nerves

Lobes

temporal

parietal

occipital

frontal

Ipsilateral vs contralateral

Limbic Lobe

VentriclesLateral

Third

Fourth

Neuro Anat - Practice

1, Sylvian fissure. 2, Globe. 3, Superior temporal gyrus. 4, Middle temporal gyrus. 5, Inferior temporal gyrus. LF, Frontal Lobe. LP, Parietal Lobe.

1, Amygdale. 2, Optic nerve. 3, Globe. 4, Inferior rectus muscle. 5, Right maxillary sinus. 6, Hippocampus. 7, Cerebellar hemisphere. 8, Transverse sinus. 9, Occipito-temporal gyri. 10, Lateral ventricle.

Neuro Anat - Practice

1, Sphenoid sinus. 2, Genu of corpus callosum. 3, Lateral ventricle. 4, Superior sagittal sinus. 5, Straight sinus.6, IVth ventricle. 7, Cerebellomedullary cistern (cisterna magna).

Neuro Anat - Practice

1, Superior frontal gyrus. 2, Middle frontal gyrus. 3, Inferior frontal gyrus. 4, Medial orbital gyrus. 5, Turbinate. 6, Gyrus rectus.

Neuro Anat - Practice

1, Hippocampus. 2, Inferior frontal gyrus. 3, Middle frontal gyrus. 4, Superior frontal gyrus. 5, Cingulate gyrus. 6, Lateral ventricle. 7, Third ventricle. 8, Middle cerebellar peduncle. 9, Medulla.

Neuro Anat - Practice

1, Superior sagittal sinus. 2, Calcarine fissure. 3, Cerebellar hemisphere. 4, Transverse sinus . 5, Straight sinus. 6, Interhemispheric fissure.

Neuro Anat - Practice

1, Optic nerve. 2, Medial rectus muscle. 3, Globe. 4, Lateral rectus muscle. 5, Right temporal lobe. 6, Pons. 7, Right occipital lobe. 8, Left occipital lobe.

Neuro Anat - Practice

1, Frontal sinus. 2, Sylvian fissure. 3, Insula. 4, 3rd ventricle. 5, Lateral ventricle. LF, Frontal Gyri. LT, Temporal gyri. LO, Occipital Gyri.

Neuro Anat - Practice

1, Genu corps callosum. 2, Superior frontal gyrus. 3, Lateral ventricle. 4, Central sulcus.

Neuro Anat - Practice