Differences between revisions 4 and 5

Target Outcome

Geometric reconstruction of a tissue of interest ready for meshing:

as a (parametric or explicit) watertight surface representation, or
as a solid geometry

Prerequisites

Include(Infrastructure/AuxiliarySoftware, "Infrastructure", 2, from="= Geometry & Mesh Generation & Manipulation =", to="= Scripting & Numerical Analysis =")

Previous Protocols

For more details, see ["Specifications/ImageSegmentation"].

Protocols

Input

Volume of tissue of interest as a binary image aligned with original MRI coordinate system (raw, without filtering and smoothing)
Surface representation of tissue of interest in STL format in MRI coordinate system (raw, without filtering and smoothing)

Procedures

-- ["aerdemir"] DateTime(2013-12-30T15:14:36Z) This section may list general purpose procedures and alternatives to utilize the same input to reach the same output. Procedures optimized for specific tissues should also be provided in here.

When starting with volume representation

Confirm the tissue volume is a raw representation (without filtering and smoothing)
Generate raw surface representation of the tissue volume
- Upload tissue volume in image segmentation software, e.g. Slicer.
- Generate water-tight triangulated surface representation (no filtering, smoothing).
- Save raw surface representation with the same file name as the volume representation except with the .stl extension.
Continue with the next section.

When starting with surface representation

Load raw surface representation of the tissue volume in MeshLab.
Smooth raw surface representation, e.g.:
- Under Filters->Smoothing->Laplacian Smooth, Select smoothing steps of 9 and uncheck all other boxes and apply. This will smooth down most jagged edges from the original file
- Under Filters->Smoothing->Two Step Smooth, Select smoothing steps of 3, Feature Angle Threashold at 60, Normal smoothing steps at 20, and Vertex Fitting steps at 20 and apply. This step further levels uneven edges
- Under Filters->Smoothing->Taubin Smooth, Select Lambda to 1, mu to 0.0, and Smoothing steps to 12, all boxes are unchecked and press apply. This step creates an overall uniform surface with few rough edges, while still keeping the shape of the initial object. Some values may vary depending on the model input, this selection works for large bones like the femur.
Parametrize and resample smoothed surface representation.
Save smooth surface representation with the same file name as the volume representation except with trailing text of 'smooth'.

When parametric geometry is needed

Output

Explicit surface representation of tissue of interest; in STL format in MRI coordinate system (processed with volume preserving smoothing)
Parametric surface representation of tissue of interest in IGES & STP format in MRI coordinate system (processed with volume preserving smoothing)
Parametric solid model of tissue of interest in IGES & STP format in MRI coordinate system (processed with volume preserving smoothing)

-  ⇤ ← Revision 4 as of 2015-06-26 13:28:29 → 
  Size: 2361
  Editor: djs252
  Comment:
+   ← Revision 5 as of 2015-11-09 18:56:22 → ⇥
  Size: 3243
  Editor: aerdemir
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-''' Smoothing Bone:'''
+=== When starting with volume representation ===
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+Line 29:
-'''     '''Open Meshlab
+ * Confirm the tissue volume is a raw representation (without filtering and smoothing)
 * Generate raw surface representation of the tissue volume
  * Upload tissue volume in image segmentation software, e.g. Slicer.
  * Generate water-tight triangulated surface representation (no filtering, smoothing).
  * Save raw surface representation with the same file name as the volume representation except with the .stl extension.
 * Continue with the next section.
-Line 28:
+Line 36:
- *  Under Filters->Smoothing->Laplacian Smooth, Select smoothing steps of 9 and uncheck all other boxes and apply.    This will smooth down most jagged edges from the original file
 * Under Filters->Smoothing->Two Step Smooth, Select smoothing steps of 3, Feature Angle Threashold at 60, Normal smoothing steps at 20, and Vertex Fitting steps at 20 and apply.  This step further levels uneven edges
 * Under Filters->Smoothing->Taubin Smooth, Select Lambda to 1, mu to 0.0, and Smoothing steps to 12, all boxes are unchecked and press apply. This step creates an overall uniform surface with few rough edges, while still keeping the shape of the initial object
Some values may vary depending on the model input, this selection works for large bones like the femur.
+=== When starting with surface representation ===

 * Load raw surface representation of the tissue volume in !MeshLab.
 * Smooth raw surface representation, e.g.:
  * Under Filters->Smoothing->Laplacian Smooth, Select smoothing steps of 9 and uncheck all other boxes and apply. This will smooth down most jagged edges from the original file
  * Under Filters->Smoothing->Two Step Smooth, Select smoothing steps of 3, Feature Angle Threashold at 60, Normal smoothing steps at 20, and Vertex Fitting steps at 20 and apply.  This step further levels uneven edges
  * Under Filters->Smoothing->Taubin Smooth, Select Lambda to 1, mu to 0.0, and Smoothing steps to 12, all boxes are unchecked and press apply. This step creates an overall uniform surface with few rough edges, while still keeping the shape of the initial object. Some values may vary depending on the model input, this selection works for large bones like the femur.
 * Parametrize and resample smoothed surface representation.
 * Save smooth surface representation with the same file name as the volume representation except with trailing text of 'smooth'.

=== When parametric geometry is needed ===