Create DISCO+DARTEL deformation field from subjectA to subjectB

This tool creates a unique deformation field (and its inverse) that aligns data from subjectA space into subjectB space, considering either DISCO+DARTEL or Native DARTEL deformations.

Description

1. Choose the type of the study (Native or AfterDISCO).
2. Select the study directory of the experiment
3. Choose the nobias of subjectA.
4. Choose the nobias of subjectB.
5. Enter the name of the template given in 02. DARTEL Template Creation

If the subjectA (subjectB) 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_A (choice_native_image_B) parameter. In this case, add the initial data (in native_image_A (native_image_B)) and the transformation representing the added border (border_nobias_A (border_nobias_B)).

The numerical parameters (final_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_A: T1 MRI Bias Corrected ( input )

nobias_B: T1 MRI Bias Corrected ( input )

choice_native_image_A: 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_A: 4D Volume ( optional, input )

initial data (without border/crop required for Morphologist)

border_nobias_A: Transformation matrix ( optional, input )

translation added to initial data to be processed in Morphologist

choice_native_image_B: 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_B: 4D Volume ( optional, input )

initial data (without border/crop required for Morphologist)

border_nobias_B: Transformation matrix ( optional, input )

translation added to initial data to be processed in Morphologist

inv_final_disp_field_A_TO_B: FFD Field defData Inversed DISCO DARTEL A TO B ( output )

final_disp_field_A_TO_B: FFD Field defData DISCO DARTEL A TO B ( output )

subjects_hierarchy: Save Subjects Hierarchy DISCO ( input )

subjects_hierarchy_DARTEL: Save Subjects Hierarchy DARTEL ( input )

vectorinterpolation: Choice ( input )

interpDISCO: Choice ( input )

interpDARTEL: Choice ( input )

displacement_field_A: FFD Field defData DISCO ( input )

inv_displacement_field_A: FFD Field defData Inversed DISCO ( input )

displacement_field_B: FFD Field defData DISCO ( input )

inv_displacement_field_B: FFD Field defData Inversed DISCO ( input )

compo_To_Tal_A: Compo To Resample To Talairach ( input )

compo_To_Tal_B: Compo To Resample To Talairach ( input )

flow_field_A: Flow Field DISCO DARTEL ( input )

flow_field_B: Flow Field DISCO DARTEL ( input )

Technical information

Toolbox : Disco

User level : 1

Identifier : create_discodartel_deffield_betweensubjects

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

Supported file formats :

template_dir :

Directory, Directory

study_dir :

Directory, Directory

nobias_A :

NIFTI-1 image, NIFTI-1 image

nobias_B :

NIFTI-1 image, NIFTI-1 image

native_image_A :

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

border_nobias_A :

Transformation matrix, Transformation matrix

native_image_B :

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

border_nobias_B :

Transformation matrix, Transformation matrix

inv_final_disp_field_A_TO_B :

GIS image, GIS image

final_disp_field_A_TO_B :

GIS image, GIS image

subjects_hierarchy :

Text file, Text file

subjects_hierarchy_DARTEL :

Text file, Text file

displacement_field_A :

GIS image, GIS image

inv_displacement_field_A :

GIS image, GIS image

displacement_field_B :

GIS image, GIS image

inv_displacement_field_B :

GIS image, GIS image

compo_To_Tal_A :

Transformation matrix, Transformation matrix

compo_To_Tal_B :

Transformation matrix, Transformation matrix

flow_field_A :

NIFTI-1 image, NIFTI-1 image

flow_field_B :

NIFTI-1 image, NIFTI-1 image