> For the complete documentation index, see [llms.txt](https://bridge-lab.gitbook.io/docs/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/registration.md).

# Registration

## Essential Concepts <a href="#essential-concepts" id="essential-concepts"></a>

* **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