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 )

threshold_mode: Choice ( input )

threshold: Integer ( optional, input )

By default the threshold is automatically computed from the image histogram

Technical information

Toolbox : Morphologist

User level : 0

Identifier : headMesh

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

Supported file formats :

t1mri_nobias :

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

histo_analysis :

Histo Analysis, Histo Analysis

head_mesh :

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

head_mask :

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

remove_mask :

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