Imaging Data: Structure And Formats

  • Images are sheets or cubes of numbers.
  • Medical image data is typically stored in DICOM or Nifti format. They include a header that contains information on the patient and/or the image characteristics.
  • An affine transformation maps the voxel location to real-world coordinates.
  • Medical image viewers allow to navigate an image, adjust contrast, and localise brain regions with respect to an atlas.

Structural MRI: Bias Correction, Segmentation and Image Registration

  • Structural MRI provides high-resolution anatomic information for neuroimaging analysis
  • Bias correction removes image inhomogeneities
  • Tissue segmentation identifies key tissue types (grey matter, white matter, cerebrospinal fluid) from T1 weighted images
  • Co-registration of MRI to other modalities can be used to analyse these images at a regional level.

Processing and analysing PET brain images

  • PET Images are reconstructed from listmode data.
  • The most commonly used PET tracers are sensitive to amyloid plaques and neurofibrillary tau tangles.
  • Full dynamic scans are acquired from the time of injection, while static scans are acquired a fixed interval after injection when the tracer has or is approaching equilibrium
  • Summing individual frames together reduces the level of noise
  • SUVR images represent the relative uptake in each voxel to a reference region, where there is likely no specific binding

Diffusion-weighted imaging (DWI)

  • Diffusion imaging is used to obtain measurements of tissue microstructure
  • DWI consists of a 4D volume, and files describing the vectors and b-values that each volume is encoding
  • The common core processing steps are: brain masking, susceptibility correction, eddy/motion correction, and modelling (tensor fitting, NODDI, etc)

Functional Magnetic Resonance Imaging (fMRI)

  • fMRI measures small signal fluctations associated with oxyhaemoglobin in the blood resulting from brain activation
  • Images can either be acquired during a task or with no task involved (resting state)
  • Key preprocessing steps include: EPI distortion correction, brain masking, smoothing, and temporal fitering
  • Network components extracted from techniques like Melodic can show key network components, but also potentially components that represent noise.

Extra: Using the Command Line

  • The command line interface is a low-level way of interacting with your computer
  • It provides more control, more reliability, and more scalability than manually interacting with a graphical user interface.
  • Paths can be specified in two ways: an absolute path and a relative path. The absolute path remains the same regardless of the current location, where the relative path will change.
  • Help can be found by typing the man command