Dartel pipeline

This pipelines estimates the DARTEL deformation from Native data (Morphologist outputs) or data deformed by Disco pipeline).

Even in Native mode, a study directory and a subjects_hierarchy file defined in the first steps of DISCO, are required.

0. Run the first steps of Preprocessing to prepare your study directory.

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

2. Select the study directory of the experiment.

3. Choose a name for the DARTEL Template.

4. If resample_in_Talairach is True, add a translation to enable the volumes resampling in Talairach referential (exple in /neurospin/hbp/Users/jlebenberg/AC_translation.trm.

5. If crop_output is True, DARTEL input grey-white maps will be cropped. Save the crop transformation in crop_dir_trm and crop_inv_trm parameters as they are required in 04. DARTEL Images Inverse Warping, Create DISCO+DARTEL deformation field toward the common space and Create DISCO+DARTEL deformation field from subjectA to subjectB.

6. Note resolution, dimensions and crop parameters of 01. Prepare grey and white maps for DARTEL as they are required in 03. DARTEL Images Warping, 04. DARTEL Images Inverse Warping, Create DISCO+DARTEL deformation field toward the common space and Create DISCO+DARTEL deformation field from subjectA to subjectB.

Be sure to have all your spm12 paths ready in your BrainVISA preferences, or the step 02. DARTEL Template Creation of Dartel will not run.

Both steps are described in DARTEL components.

Parameters

study_type: Choice ( input )

Type of the study (Native or AfterDISCO)

template_dir: DARTEL Template Dir ( output )

Directory of the DARTEL experiment

study_dir: DISCO Study Dir ( input )

Study directory of the experiment

subjects_hierarchy: Save Subjects Hierarchy DISCO ( input )

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

DISCO displacement field from subject space to common space

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

DISCO displacement field from common space to subject space

Lgrey_white_DISCO: ListOf( Grey White Mask Corrected DISCO ) ( input )

Rgrey_white_DISCO: ListOf( Grey White Mask Corrected DISCO ) ( input )

Talairach_transforms: ListOf( Transform Graph to Talairach-AC/PC-Anatomist ) ( input )

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

resample_in_Talairach: Boolean ( input )

boundingbox_min_mm: ListOf( Float ) ( input )

boundingbox_max_mm: ListOf( Float ) ( input )

isotropic_resolution_mm: Float ( input )

batch_template_location: Batch DARTEL Create Template ( output )

subjects_hierarchy_DARTEL: Save Subjects Hierarchy DARTEL ( output )

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

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

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

Technical information

Toolbox : Disco

User level : 0

Identifier : dartel_pipeline

File name : brainvisa/toolboxes/disco/processes/dartel_pipeline.py

Supported file formats :

template_dir :

Directory, Directory

study_dir :

Directory, Directory

subjects_hierarchy :

Text file, Text file

displacement_field_DISCO :

GIS image, GIS image

inv_displacement_field_DISCO :

GIS image, GIS image

Lgrey_white_DISCO :

NIFTI-1 image, NIFTI-1 image

Rgrey_white_DISCO :

NIFTI-1 image, NIFTI-1 image

Talairach_transforms :

Transformation matrix, Transformation matrix

nobias :

NIFTI-1 image, NIFTI-1 image

batch_template_location :

Matlab script, Matlab script

subjects_hierarchy_DARTEL :

Text file, Text file

flow_field :

NIFTI-1 image, NIFTI-1 image

final_disp_field :

GIS image, GIS image

inv_final_disp_field :

GIS image, GIS image