FSL Connectome.

Reorganization of FSL data into Constellation compatible data.

Description

Usage example

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

region:                          lh.inferiorparietal

probtrackx_indir:                /my/path/fsl_db/3T_fsl/omatrix1/100206

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

temp_outdir:                     /tmp 

output_connectome:               /tmp/100206/connectome_label8.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.

probtrackx_indir: Directory ( input )

Subjects directory in a FSL connectome database, where the fiber tracts files can be found.

regions_parcellation: ROI Texture ( input )

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

temp_outdir: Directory ( output )

Temporary directory where data files will be stored during importation phase.
Example: /tmp, but this directory size should be large enough to store all the temporary files during the process.

output_connectome: String ( input )

Connectivity matrix compatible with Constellation requirements.

Technical information

Toolbox : Constellation

User level : 2

Identifier : constel_fsl_connectome

File name : brainvisa/toolboxes/constellation/processes/individual_pipelines/tools_fsl/constel_fsl_connectome.py

Supported file formats :

regions_nomenclature :

Text file, Text file

probtrackx_indir :

Directory, Directory

regions_parcellation :

GIFTI file, GIFTI file, Texture

temp_outdir :

Directory, Directory