structural imaging L4

Question 1

what are the advantages and disadvantages of manual outlining for examining regional brain volume?

Answer 1

advantages:
- gold standard

disadvantage:
- time-consuming and interrupter variability

Question 2

what are the advantages and disadvantages of surface based techniques?

Answer 2

advantages:
- better registration of sulci and gyri

disadvantages:
- only works on the cortex and requires high-resolution data

Question 3

what are the advantages/disadvantages of automated segmentation of regions?

Answer 3

advantages:
- well-validated methods available

disadvantages:
- doesnt usually work on thick slices or images with poor resolution

Question 4

what are the advantages/disadvantages of voxel-based morphometry (VBM)?

Answer 4

VBM is a neuroimaging analysis technique that surveys the entire brain for changes in regional gray matter or white matter
- based on voxels rather than predefined regions.

Question 5

why is spatial normalisation required in VBM?

Answer 5

• To transform MRI data into a common standardized space for group analysis.
• To provide a common coordinate system

Question 6

how does SPM perform normalisation?

Answer 6

SPM performs normalization using affine and non-linear transformations.

Question 7

What are the problems with intensity thresholding for segmentation?

Answer 7

• Choosing threshold levels requires user intervention.
• Bias field correction is needed, as it is an MRI artifact that causes slow changes in image intensity across the brain. This means gray matter can have different intensities in different parts of the image, so thresholds won’t work without correcting this.
• Image noise can cause random regions of white matter to have low intensity, potentially leading to misclassification as gray matter

Question 8

what is modulation and why is it used?

Answer 8

Modulation is a technique used in VBM to adjust the normalized segmented volume to account for differences in head size between subjects. It ensures that voxel intensities in a modulated image represent true volumes in that position in the brain

Question 9

what is smoothing and why is it performed?

Answer 9

Smoothing is a process applied to neuroimaging data where the intensity of each voxel is averaged with the intensities of its neighboring voxels.
It is performed to:
- Account for variations in structural anatomy (even after normalization, gyri and sulci may not be in the same place).
- reduce noise
- Increase the normality of the data

Question 10

what is free surfer?

Answer 10

• a software suite for processing and analysing brain MRI images
• computationally more intensive than VBM
• uses a command line interface rather than a GUI
• Requires high-performance computing (HPC) for manageable processing times due to the large number of processing steps and surface-based analysis

Question 11

what type of results does freesurfer provide?

Answer 11

freesurfer can output various cortical measures including:
- volume
-thickness
-surface area
-curvature
-volumes of subcortical regions
- vertex wise comparison between patient and control groups