Caret6:Documentation/UserInterface/SurfaceRegistrationOperationsWindow

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Surface Registration Window

Apply Registration Map to Data File

Spherical Registration

Registers the source spherical surface to the target spherical surface. As part of this process, a Registration Map File is created that is then used to deform source data files to the target. This process requires both the source and the target contain an Anatomical Surface, a Spherical Surface, and a Border Projection File. Both the source and target border projection file must contain identically named Landmark borders that are used for aligning the surfaces during the registration process.

Source Data Files

  • Specification File Selects the source's specification file using a file selection dialog.
  • Anatomical Surface Selects the source's anatomical surface file from a list of anatomical surface files found in the selected source specification file.
  • Spherical Surface Selects the source's spherical surface file from a list of spherical surface files found in the selected source specification file.
  • Border Projection Selects the source's border projection file from a list of border projection files found in the selected source specification file.

Target Data Files

  • Specification File Selects the target's specification file using a file selection dialog.
  • Anatomical Surface Selects the target's anatomical surface file from a list of anatomical surface files found in the selected target specification file.
  • Spherical Surface Selects the target's spherical surface file from a list of spherical surface files found in the selected target specification file.
  • Border Projection Selects the target's border projection file from a list of border projection files found in the selected target specification file.

Registration Map Parameters

  • Deformation Output By default the source files are registered to the target. If desired, the target files may also be registered to the source.
  • Use Default Parameters Uses predefined registration parameters that work well for human-to-human registration.
  • Parameters From File Allows one to select a registration map file whose parameters are used in the registration.
  • Deformed File Name Prefix This prefix is prepended to the names of all data files that are registered to the target (or source).
  • Deformed Column Name Prefix This prefix is prepended to the names of all data file (label/metric/shape) column names that are registered to the target (or source).
  • Delete Intermediate Files Primarily for debugging, this preserves files that are created as part of this process.

Registration Map File Names

  • Source to Target Reg Map - If this field is left empty, the registration map file name is automatically created by the registration process. This field may be used to override the default registration map file name for the source to target registration.
  • Target to Source Reg Map - Like the above field except allows override of the default target to source registration map file name.

Spherical Registration Algorithm

  • Read the source and target data sets.
  • Verify that the border files contain the exact same number of borders.
  • Resample the source borders to the specified border sampling.
  • Resample the target borders so that they contain the same number of links as the corresponding source borders. If there is not a target border with a name matching an source border, abort the deformation process.
  • Create the names of the output deformation map and specification files.
  • Execute the FLAT or SPHERICAL DEFORMATION process which creates the deformed source surface.
  • Create the individual to atlas deformation map file. This involves projecting nodes from the atlas surface into tiles on the deformed individual surface. So each atlas node has a corresponding location in the individual's surface specified by three nodes (the node are those of an individual's triangle) and the associated barycentric areas.
  • If this is a spherical deformation, create the individual to atlas deformation field file (vectors showing deformation).
  • Deform the individual's data files to the atlas.
  • Create the atlas to individual deformation map file.
  • If this is a spherical deformation, create the atlas to individual deformation field file.
  • Deform the atlas' data file to the individual.
  • Remove any intermediate files.
  • Set the radius of the source spherical surface to that of the target spherical surface.
  • BEGIN CYCLES
  • Resample the border files. If the source and target hemispheres are different, the source borders have their X-coordinates sign flipped. Write the files as source_after_resample_<CYCLE_NUMBER>.border and target_after_resample<CYCLE_NUMBER>.border.
  • Set the radius of the source and target border files to the radius of the target sphere.
  • Load the deformation (regularly tessellated sphere) surface and set its radius to that of the target spherical surface.
  • Tessellate the target borders into the deformation spherical and label the new nodes as Landmark Nodes. Save paint, coord, and topo as "_withLandmarks" filenames. Make this target sphere the unsmoothed target deformation sphere.
  • Perform landmark-constrained smoothing on the target deformation spherical surface. In this process, landmark nodes are fixed in position and only non-landmark nodes are smoothed). Save the coordinate file as "_withLandmarks_smoothed".
  • Replace the coordinates of the target Landmark Nodes with the coordinates from the source's borders. Save the coordinate file as "_withLandmarks_initial". This is the unsmoothed source deformation sphere.
  • Perform landmark neighbor constrained smoothing of the deformation sphere. Save the coordinate file as "_withLandmarks_smoothed". This is the smoothed source deformation sphere.
  • Perform landmark neighbor constrained morphing of the deformation sphere. In this process, landmark nodes are fixed in position and only non-landmark nodes are morphed. Save the coordinate file as "_withLandmarks_morphed". This is the morphed source deformation sphere.
  • Check for crossovers in deformation sphere. If GUI operation and it is the last cycle and there are crossovers, alert user.
  • Create the deformed source surface (coordinate file, it is deformed to the atlas). Project the source coordinates to the morphed source deformation sphere (If it is the first cycle and the source and target are different hemispheres, flip the X-coordinate before projecting to the morphed source deformation sphere). Unproject using the unsmoothed target deformation sphere to created the deformed source surface. Save the coordinate file as "_sphere_cycle_".
  • If there are more cycles to run, project the source borders to the source surface and unproject them to the deformed source surface.
  • Replace the source surface with the deformed source surface created as part of the current cycle.
  • GO TO BEGIN CYCLES.

Border Projection Landmarks

Surface-based registration functions by aligning corresponding landmarks (drawn as borders) on the source and target surfaces.

The Landmark Pinned Relaxation Algorithm functions well with the Core 6 Landmarks.

The orientation, location of first and last points in the landmark borders, is very important.

See Core 6 Landmarks for more information.

Central Sulcus

Must be named LANDMARK.CentralSulcus.

On the inflated surface, the central sulcus landmark starts 19mm above the lip of the Sylvian Fissure and runs in a dorsal direction and ends 18mm from the dorsal-medial tip of the central sulcus.

(Anterior) Superior Temporal Gyrus

Must be named LANDMARK.SF_STSant.

On the inflated surface, the anterior superior temporal gyrus landmark begins at the same Y-coordinate (the Y-Axis runs posterior to anterior) as the ventral tip of the central sulcus. This landmark continues to the temporal pole.

Calcarine Sulcus

Must be named LANDMARK.CalcarineSulcus.

On the inflated surface, this landmark starts at 24mm anterior of the occipital pole and continues until it reaches, but does not cross, the medial wall landmark.

Medial Wall Dorsal Segment

Must be named LANDMARK.MedWall.DORSAL.

Medial Wall Ventral Segment

Must be named LANDMARK.MedWall.VENTRAL.

Sylvian Fissure

Must be named LANDMARK.SylvianFissure.

Images of Landmarks

Image:SurfaceBasedRegistration_CentralSulcusAndSF_STSant.jpg

Image:SurfaceBasedRegistrationMedialWallAndCalcarine.jpg

Image:SurfaceBasedRegistrationSylvianFissure.jpg

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