This lesson is still being designed and assembled (Pre-Alpha version)

sMRI Acquisition and Modalities


Teaching: 20 min
Exercises: 10 min
  • How is a structural MR image acquired?

  • What anatomical features do different modalities capture?

  • Visualize and understand differences in T1,T2,PD/FLAIR weighted images.

You Are Here!


Image acquisition

  1. The acquisition starts with application of strong magnetic field B0 (e.g. 1.5 or 3.0 Tesla > 10000x earth’s magnetic field) which forces the hydrogen nuclei of the abundant water molecules in soft tissues in the body to align with the field. You can think of hydrogen nuclei as tiny magnets of their own.

  2. Then the scanner applies a radio-frequency (RF) (i.e. excitation) pulse which tilts these nuclei from their alignment along B0. The nuclei then precess back to the alignment. The precessing nuclei emit a signal, which is registered by the receiver coils in the scanner.

  3. This signal has two components: 1) Longitudinal (z-axis along the scanner’s magnetic field) and 2) Transverse (xy-plane orthogonal to the scanner’s magnetic field).

  4. Initially the longitudinal signal is weak as most nuclei are tilted away from the z-axis. However this signal grows as nuclei realign. The time constant that dictates the speed of re-alignment is denoted by T1.

  5. Initially the transverse signal is strong as most nuclei are in phase coherence. The signal decays as the nuclei dephase as they realign. This decay is denoted by the T2 time constant.

  6. The tissue specific differences in T1 and T2 relaxation times is what enables us to see anatomy from image contrast. The final image contrast depends on when you listen to the signal (design parameter: echo time (TE)) and how fast you repeat the tilt-relax process i.e. RF pulse frequency (design parameter: repetition time (TR)).

T1 and T2 relaxation

Here we see signal from two different tissues as the nuclei are tilted and realigned. The figure on the left shows a single nucleus (i.e. tiny magnet) being tilted away and then precessing back to the the initial alighment along B0. The figure on the right shows the corresponding registered T1 and T2 signal profiles for two different “tissues”. The difference in their signal intensities results in the image contrast.


Brain tissue comparison

The dotted-black line represents the epoch when you “listen” to the signal (i.e. echo time or TE).


T1w, T2w, and PD acquisition

  TE short TE long (~ T2 of tissue of interest)
TR short (~ T1 of tissue of interest) T1w -
TR long Proton Density (PD) T2w

Note: More recently, the FLAIR (Fluid Attenuated Inversion Recovery) sequence has replaced the PD image. FLAIR images are T2-weighted with the CSF signal suppressed.

pulse sequence parameters and image contrast

What are the two basic pulse sequence parameters that impact T1w and T2w image contrasts? Which one is larger?


Repetition time (TR) and echo time (TE) are the two pulse sequence parameters that dictate the T1w and T2w image contrasts. TR > TE.

T1 and T2 relaxation times for various tissues

  T1 (ms) T2 (ms)
Bones 500 50
CSF 4000 500
Grey Matter 1300 110
White Matter 800 80

Tissue type and image contrast

In the T1w image, which one is brighter: White matter, Grey Matter, or CSF?


White Matter (i.e. axonal tracts)

T1w, T2w image contrasts

T1w T2w
T1 T2

Applications per modality

Modality Contrast Characteristics Use Cases
T1w Cerebrospinal fluid is dark Quantifying anatomy e.g. measure structural volumes
T2w CSF is light, but white matter is darker than with T1 Identify pathologies related to lesions and tumors
PD CSF is bright. Gray matter is brighter than white matter Identify demyelination
FLAIR Similar to T2 with the CSF signal suppressed Identify demyelination

Image acquisition process and parameters


What do we want?

What can we control?

Magnetic strengths 1.5T vs 3T vs 7T

MR sequences (i.e. timings of “excitation pulse”, “gradients”, and “echo acquisition” )

e.g. MPRAGE: Magnetization Prepared - RApid Gradient Echo (Commonly used in neuroimaging)

mprage Drawing

Spatial encoding of the signal


MPRAGE and k-space images Courtesy of Allen D. Elster,

Interacting with images (see this notebook for detailed example.)

import nibabel as nib
import nilearn
from nilearn import plotting
local_data_dir = '../local_data/1_sMRI_modalities/'
T1_filename = local_data_dir + 'craving_sub-SAXSISO01b_T1w.nii.gz'
T2_filename = local_data_dir +'craving_sub-SAXSISO01b_T2w.nii.gz'
T1_img = nib.load(T1_filename)
T2_img = nib.load(T2_filename)

# grab data array
T1_data = T1_img.get_fdata()
T2_data = T2_img.get_fdata()

# plot
plotting.plot_anat(T1_filename, title="T1", vmax=500)
plotting.plot_anat(T2_filename, title="T2", vmax=300)

T1w T2w
nilearn_T1 nilearn_T2

Key Points

  • Different acquisition techniques will offer better quantification of specific brain tissues