Registration

Essential Concepts

• Image Spaces (associated with distinct coordinate system)

  • Native space – coordinates unique to subject’s head placement in MRI scanner

  • Standard space – standard defined coordinates across all images in this space define anatomy location

    • Images in this space can have different resolution

• Coordinate Systems

  • Voxel coordinates

    • no units; integers

    • voxel count in each dimension reflecting matrix size

    • Origin: corner of image (e.g., 0,0,0 or 1,1,1)

    • Origin and axes naming conventions differ in programs

  • World coordinates

    • Have units in mm; floating values

    • Denote anatomy

      • Handedness system

        • Right-handed (RAS) system

          • x+ Left-Right

          • y+ Posterior-Anterior

          • z+ Inferior-Superior

          • Default for: MNI152 space, NifTi

      • LPS system

        • Default for: Dicom

  • Origin: can differ in programs, standard space (e.g., MNI152 space origin at anterior commissure)

• Standard Templates

  • RULE: Know demographics of cases used to generate atlas, try match template and study cohort

  • Talairach and Tournoux (TT space)

    • 1 postmortem brain, female, 60 years old

  • MNI152/ICBM 152 (MNI152 space)

    • 152 healthy young adults

  • Study-Specific Templates (Study Specific space)

    • Need substantial representative cases to make

• Standard Atlas

  • RULE: Know demographics of cases used to generate atlas; MAY BE DIFFER from template in same space, try match atlas, template and study cohort

  • Talairach and Tournoux (MNI152 space) - discrete

    • 1 postmortem brain, female, 60 years old

  • AAL (MNI152 space) - discrete

    • Multiple scans from 1 healthy adult

  • Harvard-Oxford (MNI152 space) - probabilistic

    • 37 healthy adults

  • JHU WM (MNI152 space) – probabilistic

    • 28 young healthy adults

Registration Decision Points

• Prep - QC input & reference images

  • Artifacts

  • Sharpness of anatomical features

  • Variability of anatomy

  • Comparable demographics (e.g., atlas, standard template, study cohort)

  • FOV sampling of body similar (e.g., amount of neck included)

• Prep - Reorient (optional)

  • Initialization

• Prep - Crop (optional)

  • Remove non brain areas in FOV in both images so sampling similar (e.g., neck)

• Prep - Brain extraction of input & reference image (optional)

  • RULE: input & reference image MUST match in skull sampling (BAD: 1 w/skull, 1 w/out)

  • Quality needs to be good, if not – better to not do

• Registration - Spatial transformations

  • DEFINITION: Calculate the best alignment of the images by determining parameters of the spatial transformation

  • Linear Transformation (within-subject, same anatomy)

    • Rigid-Body (6-DOF: 3 rotations, 3 translations)

      • Within-subject registration

      • Initializing other methods

    • Affine (12-DOF: 3 rotations, 3 translations, 3 scaling, 3 sheers/skews)

      • Eddy-current distortion correction

      • Initializing nonlinear transformations

  • Non-linear Transformation/Warp (between-subject, differ anatomy)

    • 12+ DOF

      • REQUIRE: Initialization with affine registration

• Resample/Transform – Apply the spatial transformation & creating image in new space

  • RULE: Avoid degradation of images; resample/interpolate only 1x

  • Create and check quality of separate registrations before concatenating and applying to image 1x