Deformation DISCO+DARTEL Pipeline

This tool creates an unique deformation field (i.e. considering both DISCO and DARTEL deformations) and apply it to your graph, meshes and volume.

1. Select the study directory of the experiment

2. Enter the name of the template given in 02. DARTEL Template Creation

3. Add the crop_inv_trm parameter only if you set crop_output to True in DARTEL and you saved it.

The numerical parameters (finale_isotropic_resolution, dartel_intermediate_dimension, min_x, max_X, min_y, max_Y, min_z, maxZ) and the crop_inv_trm transformation correspond to parameters in 01. Prepare grey and white maps for DARTEL.

Parameters

template_dir: DARTEL Template Dir ( input )

Directory of the DARTEL experiment

subjects_hierarchy: Save Subjects Hierarchy DISCO ( input )

final_disp_field: ListOf( FFD Field defData DISCO DARTEL ) ( input )

DARTEL or DISCO+DARTEL displacement field from subject space to common space

inv_final_disp_field: ListOf( FFD Field defData Inversed DISCO DARTEL ) ( input )

DARTEL or DISCO+DARTEL displacement field from common space to subject space

Lgraph: ListOf( Labelled Cortical folds graph ) ( input )

Rgraph: ListOf( Labelled Cortical folds graph ) ( input )

mesh_Lhemi: ListOf( Left Hemisphere Mesh ) ( input )

mesh_Lwhite: ListOf( Left Hemisphere White Mesh ) ( input )

mesh_Rhemi: ListOf( Right Hemisphere Mesh ) ( input )

mesh_Rwhite: ListOf( Right Hemisphere White Mesh ) ( input )

nobias: ListOf( T1 MRI Bias Corrected ) ( input )

Lgraph_deformed: ListOf( Labelled Cortical folds graph DISCO DARTEL ) ( output )

Rgraph_deformed: ListOf( Labelled Cortical folds graph DISCO DARTEL ) ( output )

mesh_Lhemi_deformed: ListOf( Left Hemisphere Mesh DISCO DARTEL ) ( output )

mesh_Lwhite_deformed: ListOf( Left Hemisphere White Mesh DISCO DARTEL ) ( output )

mesh_Rhemi_deformed: ListOf( Right Hemisphere Mesh DISCO DARTEL ) ( output )

mesh_Rwhite_deformed: ListOf( Right Hemisphere White Mesh DISCO DARTEL ) ( output )

nobias_deformed: ListOf( T1 MRI Bias Corrected DISCO DARTEL ) ( output )

Technical information

Toolbox : Disco

User level : 0

Identifier : deformation_disco_dartel_pipeline

File name : brainvisa/toolboxes/disco/processes/Deformation/deformation_disco_dartel_pipeline.py

Supported file formats :

template_dir :

Directory, Directory

subjects_hierarchy :

Text file, Text file

final_disp_field :

GIS image, GIS image

inv_final_disp_field :

GIS image, GIS image

Lgraph :

Graph and data, Graph and data

Rgraph :

Graph and data, Graph and data

mesh_Lhemi :

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

mesh_Lwhite :

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

mesh_Rhemi :

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

mesh_Rwhite :

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

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

Lgraph_deformed :

Graph and data, Graph and data

Rgraph_deformed :

Graph and data, Graph and data

mesh_Lhemi_deformed :

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

mesh_Lwhite_deformed :

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

mesh_Rhemi_deformed :

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

mesh_Rwhite_deformed :

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

nobias_deformed :

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