Local Shape Analysis (LSA) Workflow

Created: 2011-04-06 00:40:19      Last updated: 2011-04-06 00:40:26

This workflow takes raw un-skull-stripped volumes in 2 groups/populations and an ROI index to generate a color-coded shape object using the per-vertex local p-values of some local shape-measure (e.g., displacement, atrophy, Jacobian, curvature, etc). It also outputs the p-values color-map superimposed on the mean shape.

Problem addressed by this workflow

 

Identifying local group differences between 2 populations in one specific ROI. This workflow also generates mean-shape DX model and a CCBBM *.m file with vertex-coloring using p-values, which can be viewed as a scene in ShapeViewer. The p-values color-map is:

  • Red: p<=0.05
  • Green: 0.05<p<=0.1
  • Blue: p>0.1.

Detailed Workflow Usage & Specifications

 

  • Input: Any volumetric file format can be used for the raw unskull-stripped imput images (e.g., DICOM, Directories, Analyze, MNC, Nifti, etc.)
  • Pre-processing
    • Image conversion to Analyze
    • Converting to 8-bit
    • Intensity Inhomogeneity correction
    • Skull-stripping
    • Affine Registration
  • Auto Volume Parsing
  • Shape Modeling and Refinement
  • Computing the local Mean and Gaussian curvatures per vertex on the shape of choice for all subjects
  • Shape registration - mapping, shape-correspondences
  • Mean (atlas) shape generation
  • (Non-parametric) permutation test for statistical differences between the 2 groups locally computed on each vertex of the corresponding shapes
  • Color-coding (mapping) the p-values on the mean-shape (shape-atlas)

URL: http://www.loni.ucla.edu/twiki/bin/view/CCB/PipelineWorkflows_LSA

Information Preview

Medium

Information Run

Not available


Information Workflow Components

Not available

Information Workflow Type

LONI Pipeline

Information Uploader

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (7)

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

 

Citations (0)

None


Version History

In chronological order:



Reviews Reviews (0)

No reviews yet

Be the first to review!



Comments Comments (0)

No comments yet

Log in to make a comment




Workflow Other workflows that use similar services (0)

There are no workflows in myExperiment that use similar services to this Workflow.