Head Mesh

Extraction of the head scalp

Parameters

t1mri_nobias: T1 MRI Bias Corrected ( input )

histo_analysis: Histo Analysis ( optional, input )

head_mesh: Head Mesh ( output )

Output mesh for the scalp

head_mask: Head Mask ( optional, output )

Mask volume of the segmented head. If it is omitted or keep_head_mask is false (which is the default), the mask is not kept in the database: only the mesh is stored in the database.

keep_head_mask: Boolean ( input )

If false, the head mask is not stored into the database

remove_mask: 3D Volume ( optional, input )

Mask of voxels to exclude from the segmentation. Useful to manually remove sharp edges induced by artefacts

first_slice: Integer ( optional, input )

Optionally removes a number of sliced at the bottom of the image (where the signam is generally not very contrasted)

threshold: Integer ( optional, input )

By default the threshold is automatically computed from the image histogram

closing: Float ( optional, input )

Technical information

Toolbox : Morphologist

User level : 0

Identifier : headMesh

File name : brainvisa/toolboxes/morphologist/processes/segmentationpipeline/components/headMesh.py

Supported file formats :

t1mri_nobias :

GIS image, VIDA image, NIFTI-1 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, ECAT i image, PNG image, JPEG image, MNG image, GIF image, SPM image, ECAT v image

histo_analysis :

Histo Analysis

head_mesh :

TRI mesh, PLY mesh, MESH mesh, GIFTI file, MNI OBJ mesh

head_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

remove_mask :

GIS image, VIDA image, NIFTI-1 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, ECAT i image, PNG image, JPEG image, MNG image, GIF image, SPM image, ECAT v image