Constellation Individual Sub-Pipeline

Description

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Usage example

regions_nomenclature:            /casa/build/share/brainvisa-share-4.6/nomenclature/translation/nomenclature_desikan_freesurfer.txt

region:                          lh.inferiorparietal

complete_individual_matrix:      /my/path/brainvisa_db/subjects/001/diffusion/default_acquisition/default_analysis/default_tracking_session/connectivity_parcellation/avg/hcp/
                                 lh.inferiorparietal/matrix/001_hcp_lh.inferiorparietal_complete_matrix_smooth0.0_20.0to500.0mm.imas

individual_white_mesh:           /my/path/freesurfer_db/001/surf/bh.r.aims.white.gii

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

keep_regions:                    'lh.unknown' 'lh.bankssts' 'lh.inferiorparietal'

smoothing:                       3.0  

kmax:                            12  

normalize:                       True  

erase_matrix:                    True  

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Parameters

regions_nomenclature: Nomenclature ROIs File ( input )

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

region: OpenChoice ( input )

The study region based on regions_nomenclature file.

complete_individual_matrix: Connectivity Matrix ( input )

Connectivity matrix of the study region compatible with Constellation requirements.

individual_white_mesh: White Mesh ( input )

Freesurfer white-grey interface of the cortex.
Should not be inflated.

regions_parcellation: ROI Texture ( input )

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

keep_regions: ListOf( OpenChoice ) ( input )

Kept regions for the data analysis.

smoothing: Float ( input )

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

kmax: Integer ( input )

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

normalize: Boolean ( input )

By default the connectivity matrices values are normalized to balance any spurious weighting effects due to more connected regions or subjects, or to the tractography algorithm (number of seeds...). But sometimes we also like to see the raw connectivity matrix: in that case, uncheck this normalization.

erase_matrices: Boolean ( input )

Technical information

Toolbox : Constellation

User level : 2

Identifier : constel_individual_subpipeline

File name : brainvisa/toolboxes/constellation/processes/individual_pipelines/individual_sub_pipeline/constel_individual_subpipeline.py

Supported file formats :

regions_nomenclature :

Text file, Text file

complete_individual_matrix :

Sparse Matrix, Sparse Matrix

individual_white_mesh :

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

regions_parcellation :

GIFTI file, GIFTI file, Texture