White matter mask

Computes a binary white matter mask from fractional anisotropy image for the fiber tracking process.

Description

This process computes a white matter mask using the fractional anisotropy image and a threshold : voxels kept in the mask have a fractional anisotropy higher than the threshold. If the threshold is 0, the mask is not computed. The mask is used in the fiber tracking process to limit the voxels processed : fibers are tracked only in the voxels of the mask.

Parameters

fractional_anisotropy: Fractional Anisotropy ( input )

Fractional anisotropy image.

brain_mask: T2 Brain Mask ( input )

Brain mask used to compute the fratcional anisotropy image.

FA_threshold: Float ( input )

Value between 0 (isotrop) and 1(anistrop). Keep in the mask voxels having a fractional anisotropy lower than FA_threshold: if FA_threshold must be > 0, else the white matter mask is not computed.

white_mask: T2 White matter Mask ( output )

Output binary white matter mask.

Technical information

Toolbox : Diffusion and Tracking

User level : 1

Identifier : WhiteMatterMask

File name : brainvisa/toolboxes/connectomist/processes/Tracking Pipeline Components/WhiteMatterMask.py

Supported file formats :

fractional_anisotropy :

GIS image

brain_mask :

GIS image, Z compressed GIS image, gz compressed GIS image, VIDA image, NIFTI-1 image, gz compressed ECAT i image, MINC image, gz compressed MINC image, DICOM image, TIFF image, XBM image, PBM image, PGM image, BMP image, XPM image, PPM image, gz compressed NIFTI-1 image, TIFF(.tif) image, Graph and data, gz compressed VIDA image, Z compressed VIDA image, Z compressed ECAT i image, gz compressed ECAT v image, ECAT i image, Z compressed ECAT v image, PNG image, JPEG image, MNG image, GIF image, Z compressed SPM image, SPM image, gz compressed SPM image, ECAT v image

white_mask :

GIS image, VIDA image, NIFTI-1 image, MINC image, TIFF image, XBM image, PBM image, PGM image, BMP image, XPM image, PPM image, gz compressed NIFTI-1 image, ECAT i image, PNG image, JPEG image, MNG image, GIF image, SPM image, ECAT v image