Import FSL Connectomes.

Connectivity matrix import process from temporary directory to Brainvisa database.

Description

Usage example

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

outputs_database:                /my/path/brainvisa_db 

study_name:                      studyA  

method:                          averaged approach  

region:                          lh.inferiorparietal

fsl_connectome:                  /tmp/100206/connectome_label8.imas

min_fibers_length:               20.0  

complete_individual_matrix:      /my/path/brainvisa_db/subjects/100206/diffusion/default_acquisition/default_analysis/
                                 default_tracking_session/connectivity_parcellation/avg/studyA/lh.inferiorparietal/
                                 matrix/100206_studyA_lh.inferiorparietal_complete_matrix_smooth0.0_20.0to500.0mm.imas

Paramètres

regions_nomenclature: Nomenclature ROIs File ( entrée )

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

outputs_database: Choice ( input )

This parameter retrieves all databases with brainvisa ontology present in your configuration, the generated files will be written on the chosen one (see the documentation to add a database in the BrainVisa configuration).

study_name: OpenChoice ( input )

General name of the study.

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.

fsl_connectome: Any Type ( entrée )

Connectivity matrix compatible with Constellation requirements.

min_fibers_length: Réel ( input )

A filtering parameter to exclude low length fibers. Default to 20mm.

complete_individual_matrix: Matrice de connectivité ( sortie )

Imported connectivity matrix compatible with Constellation requirements.

Informations techniques

Toolbox : Constellation

Niveau d'utilisateur : 2

Identifiant : import_fsl_connectome

Nom de fichier : brainvisa/toolboxes/constellation/processes/individual_pipelines/tools_fsl/import_fsl_connectome.py

Supported file formats :

regions_nomenclature :

Text file, Text file

fsl_connectome :

Répertoire, ASCII results, AVI film, Aims bundles, Aims scalar features, Aperio svs, BMP image, BrainVISA session event, BrainVISA/Anatomist animation, Bucket, Bundle Selection Rules, Bval File, Bvec File, CSV file, Commissure coordinates, Config file, DEF Label Translation, DICOM image, Database Cache file, Répertoire, ECAT i image, ECAT v image, EPS file, FDF image, Fichier, FreesurferAvgCurv, FreesurferCurv, FreesurferCurvPial, FreesurferIsin, FreesurferLabel, FreesurferMGH, FreesurferMGZ, FreesurferParcellation, FreesurferPial, FreesurferSphereReg, FreesurferThickness, FreesurferWhite, GIF image, GIFTI file, GIS image, Graph, Graph and data, Gyri Model, HDF5 File, HTML, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, Hiérarchie, Analyse d'histogramme, Histogramme, Info file, JPEG image, JSON file, Label Translation, Leica scn, Log file, Maillage MESH, MINC image, MINC transformation matrix, MIRAX mrxs, MLP classifier, MNG image, MNI OBJ mesh, MP4 film, MPEG film, Matlab file, Matlab script, Minf, Moment Vector, Mrtrix tracts, NIFTI-1 image, Numpy Array, OGG film, PBM image, PDF File, PGM image, PLY mesh, PNG image, PPM image, PS file, Phase image, Plot results, Process execution event, Python Script, Quality Check Report, QuickTime film, Referential, SNNS pattern, SPM image, SQLite Database File, SVG file, SVM classifier, Sakura svslide, Selection, Series of BMP image, Series of GIF image, Series of GIS image, Series of JPEG image, Series of MNG image, Series of PBM image, Series of PGM image, Series of PNG image, Series of PPM image, Series of SPM image, Series of TIFF image, Series of TIFF(.tif) image, Series of XBM image, Series of XPM image, Sigraph Learner, Soma-Workflow workflow, Sparse Matrix, TIFF image, TIFF(.tif) image, Maillage TRI, Template model, Template model domain, Text Data Table, Text file, Texture, Trackvis tracts, Transformation matrix, Tree, VIDA image, Ventana bif, XBM image, XLS file, XLSX file, XML, XPM image, Z compressed ECAT i image, Z compressed ECAT v image, Z compressed GIFTI file, Z compressed GIS image, Z compressed MESH mesh, Z compressed MNI OBJ mesh, Z compressed PLY mesh, Z compressed SPM image, Z compressed TRI mesh, Z compressed Texture, Z compressed VIDA image, ZIP file, Zeiss czi, bz2 Matlab file, gz Matlab file, gz compressed ECAT i image, gz compressed ECAT v image, gz compressed GIFTI file, gz compressed GIS image, gz compressed MESH mesh, gz compressed MINC image, gz compressed MNI OBJ mesh, gz compressed NIFTI-1 image, gz compressed PLY mesh, gz compressed PS file, gz compressed SPM image, gz compressed TAR archive, gz compressed TRI mesh, gz compressed Texture, gz compressed VIDA image, gzipped XML, mdsm file, pickle file, siRelax Fold Energy

complete_individual_matrix :

Sparse Matrix, Sparse Matrix