Constellation Group Pipeline

Provides a clustering of a group of subjects.

Description

Generalities

Method

Usage example

regions_nomenclature:            /my/path/share/brainvisa-share-4.6/nomenclature/translation/nomenclature_desikan_freesurfer.txt

study_name:                      studyA  

new_study_name:                  group_studyA

method:                          averaged approach

region:                          lh.inferiorparietal

subjects_group:                  /my/path/brainvisa_db/subjects/group_analysis/g1/g1_group.xml

mean_individual_profiles:        '/my/path/brainvisa_db/subjects/001/diffusion/default_acquisition/default_analysis/default_tracking_session/connectivity_parcellation/avg/
                                 initiation/lh.inferiorparietal/clustering/smooth3.0/001_studyA_lh.inferiorparietal_mean_profile_20to500mm.gii'

normed_individual_profiles:      '/my/path/brainvisa_db/subjects/001/diffusion/default_acquisition/default_analysis/default_tracking_session/connectivity_parcellation/avg/
                                 initiation/lh.inferiorparietal/clustering/smooth3.0/001_studyA_lh.inferiorparietal_normed_mean_profile_20to500mm.gii'

average_mesh:                    /my/path/freesurfer_db/group_analysis/average_mesh_group/average_brain/averagebrain.white.gii

regions_parcellation:            '/my/path/freesurfer_db/group_analysis/average_mesh_group/average_brain/bh.annot.averagebrain.gii'

smoothing:                       3.0  

nb_clusters:                     12  

Parameters

regions_nomenclature: Nomenclature ROIs File ( input )

Nomenclature of the cortical parcellation used to partition the study.
Example : Freesurfer Desikan_Killiany Atlas

study_name: OpenChoice ( input )

General name of the study, links to corresponding study data in output_database to retrieve profiles computed during the individual processing.

new_study_name: String ( optional, input )

Optional name given to the group study.
Default to study_name.

method: Choice ( input )

Two methods are proposed:
(1) averaged approach to obtain an average result on the group.
(2) concatenated approach to obtain individual results across the group.

region: OpenChoice ( input )

The study region based on regions_nomenclature file.

subjects_group: Group definition ( input )

mean_individual_profiles: ListOf( Connectivity Profile Texture ) ( input )

List of the mean individual profiles of the given group of subjects.

normed_individual_profiles: ListOf( Connectivity Profile Texture ) ( input )

List of the normed individual profiles of the given group of subjects.

average_mesh: White Mesh ( input )

Freesurfer average white mesh of a group of subjects.

regions_parcellation: ListOf( ROI Texture ) ( input )

Cortical parcellation used to partition the study.
Example : Freesurfer Desikan_Killiany Atlas (?h.aparc.annot).

Implications of the choice of the method on the regions_parcellation parameter:
(1) averaged approach: the regions_parcellation parameter must be a file representing the average parcellation of the group of subjects.
(2) concatenated approach: the regions_parcellation parameter must be a list of files, each representing the individual parcellation of a subject of the group.

smoothing: Float ( input )

Degree of smoothing (in millimetres).
Default to 3.0 mm.

nb_clusters: Integer ( input )

Maximal number of clusters used to parcellate the study region.
Default to 12.

Technical information

Toolbox : Constellation

User level : 1

Identifier : constel_group_pipeline

File name : brainvisa/toolboxes/constellation/processes/group_pipeline/constel_group_pipeline.py

Supported file formats :

regions_nomenclature :

Text file, Text file

subjects_group :

XML, XML

mean_individual_profiles :

GIFTI file, GIFTI file, Texture

normed_individual_profiles :

GIFTI file, GIFTI file, Texture

average_mesh :

GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh

regions_parcellation :

GIFTI file, GIFTI file, Texture