Mean Individual Profile Normalization

Description

Remove internal connections of the cortical region and normalization of profile. This process also performs normalization of connectivity profiles by the total number of connections (the number of tracts reaching the label).

Usage example

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

region:                          lh.inferiorparietal

mean_individual_profile:         /my/path/brainvisa_db/subjects/001/diffusion/default_acquisition/default_analysis/default_tracking_session/connectivity_parcellation
                                 /avg/studyA/lh.inferiorparietal/clustering/smooth3.0/001_studyA_lh.inferiorparietal_mean_profile_20.0to500.0mm.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'

normed_individual_profile:       /my/path/brainvisa_db/subjects/001/diffusion/default_acquisition/default_analysis/default_tracking_session/connectivity_parcellation
                                 /avg/studyA/lh.inferiorparietal/clustering/smooth3.0/001_studyA_lh.inferiorparietal_normed_mean_profile_20.0to500.0mm.gii

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.

mean_individual_profile: Connectivity Profile Texture ( input )

Mean individual profile calculated from smoothed matrix.

regions_parcellation: ROI Texture ( input )

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

regions_selection: Choice ( input )

keep_regions: ListOf( OpenChoice ) ( input )

Kept regions for the data analysis.

normed_individual_profile: Connectivity Profile Texture ( output )

Mean individual profile after normalization.

Technical information

Toolbox : Constellation

User level : 2

Identifier : constel_normalize_individual_profile

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

Supported file formats :

regions_nomenclature :

Text file, Text file

mean_individual_profile :

GIFTI file, GIFTI file, Texture

regions_parcellation :

GIFTI file, GIFTI file, Texture

normed_individual_profile :

GIFTI file, GIFTI file, Texture