Create DISCO+DARTEL deformation field toward the common space

This tool creates an unique deformation field, i.e. considering both DISCO and DARTEL deformations or only DARTEL deformation (outputs in Point3Df).

1. Choose the type of the study (Native or AfterDISCO).

2. Select the study directory of the experiment

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

If the subject to be considered has been pre-processed before the Morphologist processing (add border to initial data), it is possible to estimate the global deformation field using the Other mode of the choice_native_image parameter. In this case, add the initial data (in native_image) and the transformation representing the added border (border_nobias).

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

study_type: Choice ( input )

Type of the study (Native or AfterDISCO)

template_dir: DARTEL Template Dir ( input )

Directory of the DARTEL experiment

study_dir: DISCO Study Dir ( input )

Study directory of the experiment

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

choice_native_image: Choice ( input )

Choose Morphologist nobias if data to be considered were those processed with Morphologist.

Choose Other if data to be considered were the initial data (without border/crop required for Morphologist)

native_image: ListOf( 4D Volume ) ( optional, input )

initial data (without border/crop required for Morphologist)

border_nobias: ListOf( Transformation matrix ) ( optional, input )

translation added to initial data to be processed in Morphologist

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

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

subjects_hierarchy_DISCO: Save Subjects Hierarchy DISCO ( input )

vectorinterpolation: Choice ( input )

interpolation of vector field

interpDISCO: Choice ( input )

voxels values resampling

displacement_field: ListOf( FFD Field defData DISCO ) ( input )

DISCO displacement field from subject space to common space

inv_displacement_field: ListOf( FFD Field defData Inversed DISCO ) ( input )

DISCO displacement field from common space to subject space

subjects_hierarchy_DARTEL: Save Subjects Hierarchy DARTEL ( input )

interpDARTEL: Choice ( input )

voxels values resampling

compo_To_Tal: ListOf( Compo To Resample To Talairach ) ( input )

flow_field: ListOf( Flow Field DISCO DARTEL ) ( input )

Technical information

Toolbox : Disco

User level : 1

Identifier : create_discodartel_deffield_commonspace

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

Supported file formats :

template_dir :

Directory, Directory

study_dir :

Directory, Directory

nobias :

NIFTI-1 image, NIFTI-1 image

native_image :

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

border_nobias :

Transformation matrix, Transformation matrix

final_disp_field :

GIS image, GIS image

inv_final_disp_field :

GIS image, GIS image

subjects_hierarchy_DISCO :

Text file, Text file

displacement_field :

GIS image, GIS image

inv_displacement_field :

GIS image, GIS image

subjects_hierarchy_DARTEL :

Text file, Text file

compo_To_Tal :

Transformation matrix, Transformation matrix

flow_field :

NIFTI-1 image, NIFTI-1 image