Dartel pipeline

This pipeline runs DARTEL to create an average template, and outputs the deformation fields to and from each subject. It can work in two different modes depending on study_type:

Native mode: using Morphologist outputs in the native space of each subject, i.e. implementing a DARTEL-only registration.

AfterDISCO mode: using data transformed by DISCO as input, i.e. implementing a DISCO+DARTEL registration.
Note that you should probably use the Disco and Dartel complete pipeline instead for performing a complete DISCO+DARTEL experiment in one run.

Description

The first step of the pipeline, 01. Prepare grey and white maps for DARTEL, brings all inputs in a common space, here the Talairach-AC/PC-Anatomist space, and resamples them on the same grid (same isotropic resolution, volume dimensions, and header transformations) as required by DARTEL.

The second step, 02. DARTEL Template Creation, calls the SPM method Run Dartel (create Templates) to perform the hard work. The diffeomorphic transformations are output by SPM as a flow field.

The last step, Create DISCO+DARTEL deformation field toward the common space, creates deformation fields to represent the diffeomorphic transformations between the subject spaces the common space. In the case of an AfterDISCO study type, these deformation fields are composed with the DISCO deformation fields: they represent the whole DISCO+DARTEL transformation.

Usage notes

The input of DARTEL consists of the hard grey-white classification resulting from Morphologist (Lgrey_white and Rgrey_white). This is a difference from the typical usage of DARTEL in SPM, where it uses the tissue class images that are output by SPM Segment. In particular, the SPM tissue class images are probability maps that include deep brain structures, whereas the Morphologist classification is a hard classification that focuses on the cortex.

Perspective for future work: being able to use the tissue class images from SPM Segment would certainly bring a substantial improvement to the pipeline, especially concerning the alignment of deep brain structures.

Even in Native mode, some byproducts of DISCO are needed: a study_dir can simply be created by running 01. Sulci Label Translation; Talairach_transforms can be created with 00a. Talairach transform extraction; subjects_hierarchy may also be needed, you can create it by running 01. Sulcal imprints extraction.

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 deformation field from subject space to common space

inv_displacement_field_DISCO: ListOf( FFD Field defData Inversed DISCO ) ( input )
DISCO deformation field from common space to subject space

Lgrey_white_DISCO: ListOf( Grey White Mask Corrected DISCO ) ( input )
Left grey-white classification image output by Morphologist, and transformed by DISCO if in AfterDISCO mode

Rgrey_white_DISCO: ListOf( Grey White Mask Corrected DISCO ) ( input )
Right grey-white classification image output by Morphologist, and transformed by DISCO if in AfterDISCO mode

Talairach_transforms: ListOf( Transform Graph to Talairach-AC/PC-Anatomist ) ( input )
Transformation from each subject space toward the Talairach space

nobias: ListOf( T1 MRI Bias Corrected ) ( input )
Bias-corrected T1-weighted image of each subject

resample_in_Talairach: Boolean ( input )
Should always be active unless you really know what you are doing.

boundingbox_min_mm: ListOf( Float ) ( input )
Minimum coordinates of the common template space, in millimeters relative to the AC point (Anterior Commissure), along the Left, Posterior, Superior axes, respectively (a.k.a. AIMS internal coordinates). Note that the old default was -105.0 -100.0 -110.0. You may need to use this for compatibility with older studies (until BrainVISA 5.0.x).

boundingbox_max_mm: ListOf( Float ) ( input )
Maximum coordinates of the common template space, in millimeters relative to the AC point (Anterior Commissure), along the Left, Posterior, Superior axes, respectively (a.k.a. AIMS internal coordinates).

isotropic_resolution_mm: Float ( input )
Voxel size of the common template space, in millimeters.

batch_template_location: Batch DARTEL Create Template ( output )
Where the batch .m script for calling SPM will be stored.

subjects_hierarchy_DARTEL: Save Subjects Hierarchy DARTEL ( output )

flow_field: ListOf( Flow Field DISCO DARTEL ) ( output )
The diffeomorphic transformation between each subject and the common space, represented as a flow field, its native form used by DARTEL.

final_disp_field: ListOf( FFD Field defData DISCO DARTEL ) ( output )
Deformation field going from each subject space toward the common space.

inv_final_disp_field: ListOf( FFD Field defData Inversed DISCO DARTEL ) ( output )
Deformation field going from the common space toward each subject space.

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