Final deformation applied on volume

This tool enables to deform volumes with the final deformation (DISCO, DARTEL, DISCO+DARTEL) toward a common space or from subjectA space to subjectB space created with Create DISCO+DARTEL deformation field toward the common space, Create DISCO+DARTEL deformation field from subjectA to subjectB, or Create DISCO deformation field from subjectA to subjectB.

Description

  1. Choose the type of the study.
  2. Choose the type of the data to be deformed.
  3. Select the study directory of the experiment.
  4. If data_in to be considered have been pre-processed before the Morphologist processing (add border to initial data), and if the final deformation field have been estimated from these initial data, choose Other in choice_native_data_in button and enter the initial data in native_data_in field.
  5. Choose the destination space CommonSpace or AnotherSubject.
  6. (only if AfterDARTEL or AfterDISCODARTEL) Enter the name of the DARTEL Template.
  7. If AnotherSubject, select the destination subject in data_dest (and if several subjects in data_in, repeat the destination subject)). Choose whether the destination spaces considered to estimate the final deformation fields were those of subjects that have been directly proceeded with Morphologist (choice_native_data_dest = Morphologist nobias) or those of native data (choice_native_data_dest = Other).

Parameters

study_type: Choice ( input )
Type of the study
data_type: Choice ( input )
template_dir: DARTEL Template Dir ( optional, input )
Directory of the DARTEL experiment
study_dir: DISCO Study Dir ( optional, input )
Study directory of the experiment
subjects_hierarchy: Save Subjects Hierarchy DISCO ( optional, input )
data_in: ListOf( T1 MRI Bias Corrected ) ( input )
choice_native_data_in: 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_data_in: ListOf( 4D Volume ) ( optional, input )
final_space: Choice ( input )
Destination space
data_dest: ListOf( T1 MRI Bias Corrected ) ( optional, input )
destination subject.

if several subjects in data_in, repeat the destination subject.

choice_native_data_dest: Choice ( optional, 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)

interp: Choice ( input )
voxels values resampling
vectorinterpolation: Choice ( input )
interpolation of vector field
inv_final_disp_field: ListOf( FFD Field defData Inversed DISCO DARTEL ) ( input )
data_out: ListOf( T1 MRI Bias Corrected DISCO DARTEL ) ( output )

Technical information

Toolbox : Disco

User level : 1

Identifier : final_deformation_volume

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

Supported file formats :

template_dir :
Directory, Directory
study_dir :
Directory, Directory
subjects_hierarchy :
Text file, Text file
data_in :
NIFTI-1 image, NIFTI-1 image
native_data_in :
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
data_dest :
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
inv_final_disp_field :
GIS image, GIS image
data_out :
NIFTI-1 image, NIFTI-1 image