Purpose

This module can be used for quantification of fiber bundles corresponding to the paper "Automatic Quantification of DTI Parameters along Fiber Bundles, BVM 2007". For quantification, the fiberness values stored at each fiber point are used. If the fiberness values have not been modified (e.g., by the module "SetFiberness"), the fiberness values represent the fractional anisotropy (FA) values.

Usage

This module takes one FiberSet and one XMarkerList as input. It is important that the fiber set is the output of the module FiberSetFilter3D after using the crop filter option "include + cut". The input XMarkerList must be identical to one of the two XMarkerLists which were used as inputs for the filtering. The chosen XMarkerList defines the direction of the quantification, i.e. it defines which end of the fiber bundle is considered as start region.

Tips

This module should only be used in combination with the Module FiberSetFilter3D (see example network).

Windows

Default Panel

../../../Projects/MLDiffusionMRI/Modules/MLFiberUtilsExtension/mhelp/Images/Screenshots/FiberBundleQuantification._default.png

Input Fields

inputFiberSet

name: inputFiberSet, type: MLBase

The input needs to be a FiberSet which is the result of filter operation of the module FiberSetFilter3D using the the option ?include + cut?

inputXMarkerList_1

name: inputXMarkerList_1, type: MLBase

The XMarkerList must be identical to one of the two XMarkerLists which were used as inputs for the filtering. The chosen XMarkerList defines the direction of the quantification, i.e. it defines which end of the fiber bundle is considered as start region.

Output Fields

outputFiberSetCenter

name: outputFiberSetCenter, type: MLBase

This output stores a FiberSet, that consists of only one fiber, which represents the computed center line.

outputDiagramCurves

name: outputDiagramCurves, type: MLBase

This output is holding a CurveList object containing 3 curves:

  1. curve (green): mean fiberness values (default is FA)
  2. curve (red): indicates the maximum values of the fiberness (default is FA).
  3. curve(blue): minimum values of the fiberness (default is FA)

Note: that these colors come from a Stylepalette which is plugged, as well as the CurveList, into an extDiagram (see example network). They need to be selected in this order.

outputXMarkerList

name: outputXMarkerList, type: MLBase

This output stores a XMarkerList. The Xmarkers represent all points used for computing the current fiberness values (min,max,avg).

Parameter Fields

Field Index

Apply: Trigger Min Fiberness: Float
Auto Apply: Bool Rotation: Vector4
Avg Fiberness: Float Sample Size: Integer
Avg of All Avgs: Float Scale Factor: Vector3
Avg of All Max: Float Translation: Vector3
Avg of All Min: Float  
Current Fiber Point: Integer  
Max Fiberness: Float  

Visible Fields

Sample Size

name: sampleSize, type: Integer, default: 100

Defines the number of sample points (measurements points) along the center line.

Translation

name: translationParameter, type: Vector3, default: 0 0 0

Translation of the plane which indicates the current measurement point.

Scale Factor

name: scaleFactor, type: Vector3, default: 5 0.1 5

Scale factor of the plane which indicates the current measurement point.

Rotation

name: rotationParameter, type: Vector4, default: 0 0 0 0

Rotation of the plane which indicates the current measurement point.

Current Fiber Point

name: currentFiberPoint, type: Integer, default: 0, minimum: 0, maximum: :field:`maxFiberPoint`

Selection of the current measurement point.

Avg Fiberness

name: avgFA, type: Float, default: 0

Average of all fiberness values for the current measurement point (->currentFiberPoint).

Min Fiberness

name: minFA, type: Float, default: 0

Minimum of all fiberness values for the current measurement point (->currentFiberPoint).

Max Fiberness

name: maxFA, type: Float, default: 0

Maximum of all fiberness values for the current measurement point (->currentFiberPoint).

Avg of All Avgs

name: avgFibernessOfAvg, type: Float, default: 0

Average of all average fiberness values.

Avg of All Min

name: avgFibernessOfMin, type: Float, default: 0

Average of all minimum fiberness values.

Avg of All Max

name: avgFibernessOfMax, type: Float, default: 0

Average of all maximum fiberness values.

Apply

name: applyButton, type: Trigger

Enforce an update of all outputs and parameter values.

Auto Apply

name: autoApply, type: Bool, default: FALSE

Auto update of all outputs and parameter values.