Disco pipeline

This pipeline estimates the DISCO deformation according to the study described by the preprocessing steps. Estimated deformations are applied on grey-white maps of each subject to perform the DARTEL registration based on DISCO initialization.

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. 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).

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

Each step is described in DISCO components.

Parameters

anatomical_constraints: Choice ( input )

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

study_dir: DISCO Study Dir ( input )

Study directory of the experiment.

sulci_to_be_studied: Sulci To Be Studied DISCO ( input )

File describing the experiment.

bundles_to_be_studied: Bundles To Be Studied DISCO ( optional, input )

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

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

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

t1mri_nobias: ListOf( T1 MRI Bias Corrected ) ( input )

Lbundles_Volume: ListOf( Bundles Volume ) ( optional, input )

Rbundles_Volume: ListOf( Bundles Volume ) ( optional, input )

Lgrey_white: ListOf( Left Grey White Mask ) ( input )

Rgrey_white: ListOf( Right Grey White Mask ) ( input )

label_translation: Label translation ( input )

Choose the sulci_model_2008.trl or /neurospin/hbp/Users/jlebenberg/sulci_model_2008_jl.trl file (in the latter, S.R.sup and S.intraCing. sulci are considered).

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

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

Technical information

Toolbox : Disco

User level : 0

Identifier : disco_pipeline

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

Supported file formats :

study_dir :

Directory, Directory

sulci_to_be_studied :

Text file, Text file

bundles_to_be_studied :

Text file, Text file

Lgraph :

Graph and data, Graph and data

Rgraph :

Graph and data, Graph and data

Talairach_transforms :

Transformation matrix, Transformation matrix

t1mri_nobias :

NIFTI-1 image, NIFTI-1 image

Lbundles_Volume :

NIFTI-1 image, NIFTI-1 image

Rbundles_Volume :

NIFTI-1 image, NIFTI-1 image

Lgrey_white :

NIFTI-1 image, NIFTI-1 image

Rgrey_white :

NIFTI-1 image, NIFTI-1 image

label_translation :

Label Translation, Label Translation

Lgrey_white_DISCO :

NIFTI-1 image, NIFTI-1 image

Rgrey_white_DISCO :

NIFTI-1 image, NIFTI-1 image