Caret7:Development/DataTypes

From Van Essen Lab

(Difference between revisions)
Jump to: navigation, search
(Caret7 DataTypes)
(Border/Contour)
Line 60: Line 60:
* Drawable by user
* Drawable by user
* Ability to assign label/metric inside
* Ability to assign label/metric inside
-
*  
+
* Has
-
 
+
** Name
 +
** Color
 +
** Metadata?
== Surface ==
== Surface ==
== Anatomy Volume ==
== Anatomy Volume ==

Revision as of 19:01, 2 August 2011

Contents

Caret7 DataTypes

Scalar/Metric

  • Voxel and vertexwise continuous scalar values.
  • Can be surface (GIFTI), volume (NIFTI), or combined (CIFTI-Dense Timeseries format).
  • Represented internally as CIFTI with original header stored in an array for saving as original file type.
  • For volumes, use implicit or explicit masking (i.e. only store data not equal to zero, or user provides a binary mask file).
  • Ability to save as CIFTI dense timeseries or export to NIFTI volume or GIFTI scalar.
  • Do not composite columns unless requested to do so by user.
  • The user will choose Scalar/Metrics on a per window basis (allow at least 10)
  • Display settings on a per column basis
  • Ability to animate through columns/step through them one at a time (i.e. current dense timeseries functionality)
  • Ability to click on a voxel or vertex and display timeseries graph
  • Ability to display average and eigen timeseries graph for arbitrary ROI
  • Ability to export timecourse for point or arbitrary ROI

Label/Parcellation

  • Voxel and vertexwise labeled integer values
  • Each integer is associated with:
    • Name
    • Color
    • Metadata?
  • Can be surface (GIFTI), volume (NIFTI), or combined (CIFTI-Parcellation*).
  • Represented internally as CIFTI with original header stored in an array for saving as original file type.
  • For volumes, use implicit or explicit masking (i.e. only store data not equal to zero, or user provides a binary mask file).
  • Ability to save as CIFTI parcellation* or export to NIFTI volume or GIFTI label.
  • The user will choose Scalar/Metrics on a per window basis (allow at least 10)
  • Ability to turn on and off different parcels, edit their names, colors, metadata
  • Ability to override medial wall
  • Ability to create labels/parcels in surfaces and volumes using ROI tools
  • Ability to convert single label/parcel to binary (1 is in, 0 is out) scalar file

*A CIFTI-parcellation is simply the header of a parcellated timeseries or connectome file. It stores the vertices and voxels that define each parcel, their names, their colors, and any relevant metadata.

Dense Connectivity

  • Voxel and vertexwise connectivity values
  • Too big to load into RAM (load on demand)
  • At least 8 connectivity entries
  • Point and click interaction on surface, volume, volume-surface-outline
  • Ability to freeze point and click and explore the values in the node
  • Ability to export connectivity map to Scalar/Metric
  • Ability to average connectivity across subjects or a arbitrary ROI
  • Consider Dense Timeseries for very high temporal density signals (e.g. lowTR BOLD, MEG/EEG) with very large files, otherwise dense timeseries functionality subsumed into metric/scalar
  • Trajectory: #samples for each modeled fiber + distance from starting point

Vector

  • Voxel and vertexwise vectors
  • Uses:
    • Surface Normals (1 per vertex)
    • Modeled Fiber orientations 3+ per diffusion space voxel (not necessarily the same as anatomy volume)
      • Display on volume slices (2D viewer) as needles
      • Display on surface slices (3D viewer) as needles
      • Color by orientation
      • Color by number
      • fODFs?
    • Gradient Vector (vertices and voxels) for design purposes, currently not used
    • Registration Vector (vertices and voxels) for design purposes, currently not used (represent connectivity-based registration deformation fields?)

Border/Contour

  • Drawable by user
  • Ability to assign label/metric inside
  • Has
    • Name
    • Color
    • Metadata?

Surface

Anatomy Volume

Personal tools
Sums Database