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.

Parameters

session_dir: Directory ( input )

t1mri: Raw T1 MRI ( output )

normalization_type: Choice ( input )

normalization_source_image: Raw T1 MRI ( optional, input )

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

use_fsl: Boolean ( input )

referential: Referential of Raw T1 MRI ( output )

t1mri_nobias: T1 MRI Bias Corrected ( output )

split_brain: Split Brain Mask ( output )

skull_stripped: Raw T1 MRI Brain Masked ( output )

skull_stripped_template: anatomical Template ( input )

template_to_mni_transform: Transformation matrix ( optional, input )

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

normalized_referential: Referential ( input )

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

spm_transformation: SPM2 normalization matrix ( output )

normalized_t1mri: Raw T1 MRI ( output )

commissure_coordinates: Commissure coordinates ( output )

histo_analysis: Histo Analysis ( output )

histo: Histogram ( output )

left_grey_white: Left Grey White Mask ( output )

right_grey_white: Right Grey White Mask ( output )

left_white_mesh: Left Hemisphere White Mesh ( output )

right_white_mesh: Right Hemisphere White Mesh ( output )

left_pial_mesh: Left Hemisphere Mesh ( output )

right_pial_mesh: Right Hemisphere Mesh ( output )

transform_chain_ACPC_to_Normalized: ListOf( Transformation ) ( input )

acpc_referential: Referential ( optional, input )

histo_undersampling: Choice ( input )

run_morphologist: Choice ( input )

Technical information

Toolbox : Morphologist

User level : 2

Identifier : import_mcribs_dhcp_preterm

File name : brainvisa/toolboxes/morphologist/processes/tools/import_mcribs_dhcp_preterm.py

Supported file formats :

session_dir :

Directory, Directory

t1mri :

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

normalization_source_image :

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

input_normalization :

Transformation matrix, Transformation matrix

referential :

Referential, Referential

t1mri_nobias :

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

split_brain :

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

skull_stripped :

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

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 :

Histo Analysis, Histo Analysis

histo :

Histogram, Histogram

left_grey_white :

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

right_grey_white :

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

left_white_mesh :

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

right_white_mesh :

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

left_pial_mesh :

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

right_pial_mesh :

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

transform_chain_ACPC_to_Normalized :

Transformation matrix, Transformation matrix

acpc_referential :

Referential, Referential