FiberSetFilter3D

MLModule
genre FiberTracking
authors Simon Hermann, Jan Klein
package FMEwork/Release
dll MLFiberUtils
definition MLFiberUtils.def
keywords DTI, Fiber, Tracking, FiberTracking, Filter, Filtering, Cropping

Purpose

The module this filters a fiber set on base of two given marker sets and a Boolean relation between those markers.

Details

Note that the filtering is performed by checking whether fibers run through spherical volumes defined by by the markers.

The density of the markers and more important, the stored radii defining the spherical volumes depend on the voxel image those markers were generated from. If the markers have been generated otherwise (e.g. by scripting), make sure to choose a sufficient large radius.

Otherwise, it is possible that the fibers run through a set of markers without being detected for filtering.

Windows

Default Panel

../../../Modules/ML/MLDiffusionMRI/MLFiberUtils/mhelp/Images/Screenshots/FiberSetFilter3D._default.png

Input Fields

If using Include (And), the "and" operation is based on the "voxel write type" of each XMarker.

The voxel write value of CSOs can be configured in the CSOManager. By default, it is set to module, which means that the foreground value of the module (CSOVoxelizeContours) is set as the voxel value of resulting voxels.

With the CSOManager and/or the CSOFreehandProcessor, the voxel write value can be set differently, for example to the id of the CSOs. Then, the voxel values in the resulting image are set to the value of the id of the CSO (if not to the background value). By that, it is possible to reconstruct the origin of a voxel (by which CSO it was enclosed).

inputFiberSet

name: inputFiberSet, type: MLBase

The fiber set to be filtered.

inputXMarkerList_1

name: inputXMarkerList_1, type: MLBase

The marker set to filter the input fibers.

inputXMarkerList_2

name: inputXMarkerList_2, type: MLBase

An additional marker set that is only used for the operation INCLUDE_CUT.

Output Fields

outputFiberSet

name: outputFiberSet, type: MLBase

The filtered fiber set.

Parameter Fields

Field Index

Apply: Trigger
Auto Apply: Bool
Auto Update: Bool
Output Num Filtered Fibers: Integer
Type of Merging: Enum
Update: Trigger

Visible Fields

Output Num Filtered Fibers

name: numFibers, type: Integer, persistent: no

Shows the number of output fibers after filtering the input fiber set.

Apply

name: applyButton, type: Trigger

If pressed, the module computes anew.

Auto Apply

name: autoApply, type: Bool, default: FALSE

If checked, the module computes anew on any parameter change.

Auto Update

name: autoUpdate, type: Bool, default: TRUE

If checked, the module computes anew on any input change.

Update

name: updateButton, type: Trigger

If pressed, the module computes anew.

Type of Merging

name: switchUnionIntersection, type: Enum, default: Include (Or)

Defines the type of filtering operation on the fibers.

Values:

Title Name Description
Include (And) Include (And) Only fibers remain that run through all markers of the first marker list.
Include (Or) Include (Or) Only fibers remain that run through any markers of the first marker list.
Include + Cut Include + Cut Only fibers remain that run between markers of both marker lists.
Exclude Exclude Only fibers remain that run through no markers of the first marker list.
No Filter No Filter Copies the original input fiber set.