Smoothing of the Individual Matrix.

Smoothing of the connectivity matrix resulting from the preprocessing of tractography data.

Description

There are two matrices, one for each type of fibers (labeled fibers or semilabeled fibers), and subsequently summed to give complete connectivity matrix (labelled patch vertices, cortex vertices). Sparse matrix smoothing using heat diffusion, with the geometry of a mesh.

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/studyA/lh.inferiorparietal/matrix/001_studyA_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

smoothing:                       3.0  

complete_matrix_smoothed:        /my/path/brainvisa_db/subjects/001/diffusion/default_acquisition/default_analysis/default_tracking_session/connectivity_parcellation
                                 /avg/studyA/lh.inferiorparietal/matrix/001_studyA_lh.inferiorparietal_complete_matrix_smooth3.0_20.0to500.0mm.imas

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 after preprocessing.

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).

smoothing: Float ( input )

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

complete_matrix_smoothed: Connectivity Matrix ( output )

Smoothed connectivity matrix.

Technical information

Toolbox : Constellation

User level : 2

Identifier : constel_smooth_matrix

File name : brainvisa/toolboxes/constellation/processes/individual_pipelines/individual_sub_pipeline/tools/constel_smooth_matrix.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

complete_matrix_smoothed :

Sparse Matrix, Sparse Matrix