Extract connected components in order

This process propose to extract connected components of a binary data volume in the selected order.
It enables to order the extracted components int the coronal, sagittal and axial plane.

Figure 1: Section arrangements on different planes (coronal, sagittal and axial).


Figure 2: All possible section arrangement on the coronal plane according to X axis first.


Figure 3: All possible section arrangement on the coronal plane according to Y axis first.


Figure 4: the 3D arrangement of the coronal plane.

Parameters

Input_Binary_Volume: 3D Volume ( input )

Upload the binary data volume

Number_Of_Components: Integer ( input )

Enter the number of components to be extracted

Plane: Choice ( input )

Select the plane of arrangement (coronal, sagittal or axial) in which the components have been arranged (Figure 1)

Global_Arrangement: Choice ( input )

Choose the global arrangement on plane (Figure 2 and 3)

Local_Arrangement: Choice ( input )

Choose the local arrangement on plane (Figure 2 and 3)

Plane_Order: Choice ( input )

Select the 3D arrangement of plane (Figure 4)

Number_Of_Components_X: Integer ( input )

Enter the number of components on the X-axis

Number_Of_Components_Y: Integer ( input )

Enter the number of components on the Y-axis

Number_Of_Components_Z: Integer ( input )

Enter the number of components on the Z-axis

Output_Label_Volume: 3D Volume ( output )

Specify the output directory and enter the output file name.

Technical information

Toolbox : Bioprocessing

User level : 3

Identifier : ExtractComponentsInOrder

File name : brainvisa/toolboxes/bioprocessing/processes/research/toolbox/ExtractComponentsInOrder.py

Supported file formats :

Input_Binary_Volume :

gz compressed NIFTI-1 image, Aperio svs, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, Ventana bif, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

Output_Label_Volume :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image