01. Sulcal imprints extraction

This process extracts the sulcal imprints from the Labelled Cortical Folds Graph of each subject.

You probably want to use this process as part of Disco and Dartel complete pipeline or Disco pipeline instead of using it in isolation.

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

Select the sulci graphs associated to subjects to be registered.

Select the study directory of the experiment.

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).

Parameters div_pt_cloud_H and div_pt_cloud_B allow to modulate the number of points in the imprints. Higher values give less detailed imprints, while smaller values give more detailed imprints. (see below for more details)

max_BL parameter is an arbitrary value to differenciate hull junction and bottom sulcal imprints. Change if numerous sulci are added to the model.

ldk_type parameter enables to base the registration only on hull junctions (in this case select 'H'), only on bottoms (in this case select 'B'), or both (in this case select 'B+H'). For DISCO based on bundles only, choose 'H'.

In addition to sulcal imprints, this process creates a text file to summarize the hierarchy of all studied subjects (subject_hierarchy). This file will be used in other steps.

This process also has other outputs, which are not shown at the level of the BrainVISA process:
DISCO_{Study}
└── deformed_output
    └── {subject}-{acquisition}-{analysis}-folds-{graph_version}
        └── {sulci_recognition_session}_auto / {sulci_recognition_session}_manual
            └── mesh
                └── imprint_workspace.mat

Parameters

anatomical_constraints: Choice ( input )
Choose constraints to drive the deformation (bundles are work in progress...).

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

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

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

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

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

study_dir: DISCO Study Dir ( input )
Select the study directory of the experiment

sulci_to_be_studied: Sulci To Be Studied DISCO ( input )

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

sulci_label_translation_siGraph: Sulci Label Translation siGraph DISCO ( input )

left_imprint_mesh: ListOf( Sulcal Imprint Full Mesh ) ( output )

left_imprint_texture: ListOf( Sulcal Imprint Full Texture ) ( output )

left_imprint_bottom: ListOf( Sulcal Imprint Full Bottom ) ( output )

left_imprint_hull_junction: ListOf( Sulcal Imprint Full Hull Junction ) ( output )

right_imprint_mesh: ListOf( Sulcal Imprint Full Mesh ) ( output )

right_imprint_texture: ListOf( Sulcal Imprint Full Texture ) ( output )

right_imprint_bottom: ListOf( Sulcal Imprint Full Bottom ) ( output )

right_imprint_hull_junction: ListOf( Sulcal Imprint Full Hull Junction ) ( output )

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

div_pt_cloud_H: Float ( input )
Simplification factor for the Hull Junction imprints. Higher values give less detailed imprints, while smaller values give more detailed imprints.
In detail: the imprint is initialized to the set of N points that are contained in the Hull Junction bucket. This point cloud is then simplified to K centroids using a K-means algorithm, where K = floor(N / div_pt_cloud_H) + 1.

Please note that sulcal graphs contain a thick representation of the Hull Junction (typically more than 1 voxel thickness), which means that a higher value of div_pt_cloud_H is needed to obtain a similar imprint resolution compared to div_pt_cloud_B.

div_pt_cloud_B: Float ( input )
Simplification factor for the Bottom imprints. Higher values give less detailed imprints, while smaller values give more detailed imprints.
In detail: the imprint is initialized to the set of N points that are contained in the Bottom bucket. This point cloud is then simplified to K centroids using a K-means algorithm, where K = floor(N / div_pt_cloud_B) + 1.

Please note that sulcal graphs contain a very thin representation of the Bottom (1 voxel thickness), which means that a lower value of div_pt_cloud_B is needed to obtain a similar imprint resolution compared to div_pt_cloud_H.

max_BL: Integer ( input )
Arbitrary value to differenciate hull junction and bottom sulcal imprints. Increase this value if numerous sulci are added to the model.

ldk_type: Choice ( input )
To base the registration only on hull junctions ('H'), only on bottoms ('B'), or both ('B+H'). For DISCO based on bundles only, choose 'H'.

best_way_criteria: Choice ( input )

subjects_hierarchy: Save Subjects Hierarchy DISCO ( output )
Text file to summarize the hierarchy of all studied subjects; used in other steps.

Technical information

Toolbox : Disco

User level : 0

Identifier : sulcalImprintGroup

File name : brainvisa/toolboxes/disco/processes/DISCO_components/sulcalImprintGroup.py

Supported file formats :
Lgraph :
Graph and data, Graph and data
Rgraph :
Graph and data, Graph and data
t1mri_nobias :
NIFTI-1 image, NIFTI-1 image
Lbundles_Volume :
NIFTI-1 image, NIFTI-1 image
Rbundles_Volume :
NIFTI-1 image, NIFTI-1 image
study_dir :
Directory, Directory
sulci_to_be_studied :
Text file, Text file
bundles_to_be_studied :
Text file, Text file
label_translation :
Label Translation, Label Translation
sulci_label_translation_siGraph :
Text file, Text file
left_imprint_mesh :
MESH mesh, MESH mesh
left_imprint_texture :
Texture, Texture
left_imprint_bottom :
NIFTI-1 image, NIFTI-1 image
left_imprint_hull_junction :
NIFTI-1 image, NIFTI-1 image
right_imprint_mesh :
MESH mesh, MESH mesh
right_imprint_texture :
Texture, Texture
right_imprint_bottom :
NIFTI-1 image, NIFTI-1 image
right_imprint_hull_junction :
NIFTI-1 image, NIFTI-1 image
Talairach_transform :
Transformation matrix, Transformation matrix
subjects_hierarchy :
Text file, Text file