Import MCRIBS dHCP preterm subject into a brainvisa database

Import the outputs of the MCRIBS segmentation tool dedicated to babies T2 MRI images, and generate a Morphologist-compatible dataset.

Description

It supports dHCP processed images, and work is in progress to support outputs of the dHCP MCRIBS anatomical pipeline, which appaently produces results in a different shape.

Paramètres

session_dir: Répertoire ( entrée )

t1mri: Raw T1 MRI ( sortie )

normalization_type: Choice ( input )

normalization_source_image: Raw T1 MRI ( optional, entrée )

input_normalization: Transform Raw T1 MRI to Talairach-MNI template-SPM ( optional, entrée )

use_fsl: Booléen ( input )

referential: Referential of Raw T1 MRI ( sortie )

t1mri_nobias: IRM T1 Biais Corrigé ( sortie )

split_brain: Séparation du masque du cerveau ( sortie )

skull_stripped: Raw T1 MRI Brain Masked ( sortie )

skull_stripped_template: anatomical Template ( entrée )

template_to_mni_transform: Transformation matrix ( optional, entrée )

mni_transform: Transform Raw T1 MRI to Talairach-MNI template-SPM ( sortie )

normalized_referential: Referential ( entrée )

talairach_transformation: Transform Raw T1 MRI to Talairach-AC/PC-Anatomist ( sortie )

spm_transformation: SPM2 normalization matrix ( sortie )

normalized_t1mri: Raw T1 MRI ( sortie )

commissure_coordinates: Commissure coordinates ( sortie )

histo_analysis: Analyse d'histogramme ( sortie )

histo: Histogramme ( sortie )

left_grey_white: Left Grey White Mask ( sortie )

right_grey_white: Right Grey White Mask ( sortie )

left_white_mesh: Left Hemisphere White Mesh ( sortie )

right_white_mesh: Right Hemisphere White Mesh ( sortie )

left_pial_mesh: Left Hemisphere Mesh ( sortie )

right_pial_mesh: Right Hemisphere Mesh ( sortie )

transform_chain_ACPC_to_Normalized: ListOf( Transformation ) ( input )

acpc_referential: Referential ( optional, entrée )

histo_undersampling: Choice ( input )

run_morphologist: Choice ( input )

Informations techniques

Toolbox : Morphologist

Niveau d'utilisateur : 2

Identifiant : import_mcribs_dhcp_preterm

Nom de fichier : brainvisa/toolboxes/morphologist/processes/tools/import_mcribs_dhcp_preterm.py

Supported file formats :

session_dir :

Répertoire, Répertoire

t1mri :

gz compressed NIFTI-1 image, DICOM image, Répertoire, 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

normalization_source_image :

gz compressed NIFTI-1 image, Aperio svs, DICOM image, Répertoire, 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

input_normalization :

Transformation matrix, Transformation matrix

referential :

Referential, Referential

t1mri_nobias :

gz compressed NIFTI-1 image, DICOM image, Répertoire, 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

split_brain :

gz compressed NIFTI-1 image, DICOM image, Répertoire, 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

skull_stripped :

gz compressed NIFTI-1 image, DICOM image, Répertoire, 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

skull_stripped_template :

NIFTI-1 image, MINC image, NIFTI-1 image, SPM image

template_to_mni_transform :

Transformation matrix, Transformation matrix

mni_transform :

Transformation matrix, Transformation matrix

normalized_referential :

Referential, Referential

talairach_transformation :

Transformation matrix, Transformation matrix

spm_transformation :

Matlab file, Matlab file

normalized_t1mri :

NIFTI-1 image, NIFTI-1 image, SPM image

commissure_coordinates :

Commissure coordinates, Commissure coordinates

histo_analysis :

Analyse d'histogramme, Analyse d'histogramme

histo :

Histogramme, Histogramme

left_grey_white :

gz compressed NIFTI-1 image, DICOM image, Répertoire, 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

right_grey_white :

gz compressed NIFTI-1 image, DICOM image, Répertoire, 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

left_white_mesh :

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

right_white_mesh :

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

left_pial_mesh :

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

right_pial_mesh :

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

transform_chain_ACPC_to_Normalized :

Transformation matrix, Transformation matrix

acpc_referential :

Referential, Referential