Disco and Dartel complete pipeline

This pipeline enables to chain both DISCO and DARTEL registrations. It also applies the display fields to your graph, meshes and volume (afterDISCO and afterDISCODARTEL).

0. Run the first steps of Preprocessing to prepare your study directory. Run 00. Copy DISCO/DARTEL inputs in a compatible format if your data are not in 'nifti' (format required for DISCO processing).

1. Choose which constraints will drive the deformation (bundles still in progress...).

2. Select the study directory of the experiment.

3. Select the sulci graphs associated to subjects to be registered.

4. Give a name to the DARTEL Template.

5. In the label_translation field, you should select the sulci_model_2008.trl file or the /neurospin/hbp/Users/jlebenberg/sulci_model_2008_jl.trl file (in the latter, S.R.sup and S.intraCing. sulci are considered).

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

7. 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.

Be sure to have your Matlab path and executable set to Matlab 2014a in your BrainVisa preferences when you want to use DISCO. Also, 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.

All the pipelines are described in Disco pipeline, Deformation DISCO Pipeline, Dartel pipeline and Deformation DISCO+DARTEL Pipeline.

Parameters

anatomical_constraints: Choice ( input )

template_dir: DARTEL Template Dir ( output )

Directory of the DARTEL experiment

study_dir: DISCO Study Dir ( input )

Lgraph: ListOf( Labelled Cortical folds graph ) ( input )

label_translation: Label translation ( input )

sulci_to_be_studied: Sulci To Be Studied DISCO ( input )

boundingbox_min_mm: ListOf( Float ) ( input )

boundingbox_max_mm: ListOf( Float ) ( input )

isotropic_resolution_mm: Float ( input )

Technical information

Toolbox : Disco

User level : 0

Identifier : DISCO_DARTEL_Complete_pipeline

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

Supported file formats :

template_dir :

Directory, Directory

study_dir :

Directory, Directory

Lgraph :

Graph and data, Graph and data

label_translation :

Label Translation, Label Translation

sulci_to_be_studied :

Text file, Text file