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 )

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, 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

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, 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

remove_mask :

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