Structural MRI

Question 1

T2 weighted MRI

Answer 1

• Imaging modality with longer TE and TR times
• Air and bone appear dark, while CSF, blood and edema appear bright.
• contrast and brightness are predominately determined by the T2 properties of tissue.

Question 2

T1 weighted MRI

Answer 2

• Image modality with short Time Echo (TE) and short rotation time (TR).
• CSF appears dark
• Basic pulse sequences in MRI and demonstrates differences in the T1 relaxation times of tissues.

Question 3

Main steps in structural MRI process

Answer 3

1. scan acquisition (patient in machine)
2. Data representation in binary
3. Use visualization software to represent data as image
4. Analysis with software
5. statistical analysis

Question 4

Motion artifacts

Answer 4

• A problem in structural and functional MRI.
• Higher motion = lower gray matter volume estimates
• Post hoc: exclude scans with high motion; new correction approaches for DTI data

Question 5

Voxel-wise lesion-symptom mapping, 3 approaches:

Answer 5

1. lesion-defined
   - behavioral performance of a group of patients with a common area of injury
2. behavior-defined
   - patients are grouped according to whether or not they show a specific behavioral deficit
3. mass-univariate
   - does not require patients to be grouped by either lesion site or behavioral cutoff a priori
   - for each voxel, patients are categorized according to whether they did or did not have a
   lesion affecting that voxel

Question 6

Manual volumetry

Answer 6

Manual

   - Remains the gold standard for assessing changes in brain volume
   - ITK-Snap : hand-selected regions
   - Labor intensive!

Question 7

Automated volumetry

Answer 7

pros:
- faster,
- more reliable,
- standardized

cons:

• Freesurfer can overestimate total hippocampal volumes
• Problems with accurately detecting boundaries between hippocampus and neighboring structures

Question 8

FSL F.I.R.S.T. automated segmentation

Answer 8

“FMRIB’s Integrated Registration & Segmentation Tool”

• model-based segmentation of subcortical structures
• shape/appearance (intensity) models constructed from manually segmented images (training data)

Question 9

Voxel-based morphometry:

Answer 9

• voxel-wise analysis of the local concentration of gray matter
• align images globally and compare GM likelihood at each voxel
• 1. brain extraction 2. segmentation 3. normalization 4. smoothing

Question 10

Spatial smoothing

Answer 10

• Why?: makes each voxel more similar to its neighbors

- Spatial normalization is not perfect, and smoothing helps accommodate inter-individual differences in local anatomy

Question 11

Voxel-based morphometry Example study:

Answer 11

London Taxi drivers showed increase in gray matter density in posterior hippocampi with
concomitant changes to their memory profile

Question 12

Cortical thickness

Answer 12

Measuring the highly-folded outer layer of grey matter with Free Surfer.
Shortest distance between white matter surface and pial
surfaces
→ 1-5 mm in healthy subjects

Question 13

Cortical thickness estimation (FreeSurfer)

Answer 13

Pros: 
- automated, continuous, whole cortex
- direct, biologically meaningful measure in millimeters
Cons:
- heavy post-processing (6-24 hours/scan)
-  dependent on classification
- manual corrections often necessary
- limited to (neo)cortex