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compute_region_centres
compute_region_centres
 
 
parcellations
parcellations
 
 
read_and_write_func
read_and_write_func
 
 
remesher
remesher
 
 
subparcel
subparcel
 
 
uniform_parcellate
uniform_parcellate
 
 
.gitignore
.gitignore
 
 
.travis.yml
.travis.yml
 
 
HCP_pre_scripts.sh
HCP_pre_scripts.sh
 
 
LICENSE.txt
LICENSE.txt
 
 
README.md
README.md
 
 
aseg2srf
aseg2srf
 
 
average_orientations.txt
average_orientations.txt
 
 
check_correspondance_diff_parcellation.m
check_correspondance_diff_parcellation.m
 
 
check_region_mapping.py
check_region_mapping.py
 
 
compute_connectivity_files.py
compute_connectivity_files.py
 
 
compute_connectivity_parcellation_96.m
compute_connectivity_parcellation_96.m
 
 
compute_connectivity_sub.py
compute_connectivity_sub.py
 
 
compute_region_centres.m
compute_region_centres.m
 
 
compute_region_centres.prj
compute_region_centres.prj
 
 
correct_region_mapping.py
correct_region_mapping.py
 
 
correspondance_mat.txt
correspondance_mat.txt
 
 
correspondance_mat_96.txt
correspondance_mat_96.txt
 
 
cortical.txt
cortical.txt
 
 
custom_connectivity_matrix.py
custom_connectivity_matrix.py
 
 
custom_connectome.sh
custom_connectome.sh
 
 
example_config.sh
example_config.sh
 
 
export_to_vertices.py
export_to_vertices.py
 
 
extract_bem.py
extract_bem.py
 
 
extract_high.py
extract_high.py
 
 
fs_region.txt
fs_region.txt
 
 
lh_ref_table.txt
lh_ref_table.txt
 
 
list_subcortical.py
list_subcortical.py
 
 
main_region.sh
main_region.sh
 
 
main_surface.sh
main_surface.sh
 
 
matlab_deploy.m
matlab_deploy.m
 
 
name_regions.txt
name_regions.txt
 
 
name_regions_cortical.txt
name_regions_cortical.txt
 
 
name_regions_subcortical.txt
name_regions_subcortical.txt
 
 
off2txt.py
off2txt.py
 
 
read_mrtrix_tracks.m
read_mrtrix_tracks.m
 
 
reference_table_freesurfer.ods
reference_table_freesurfer.ods
 
 
region_mapping.py
region_mapping.py
 
 
region_mapping_other_parcellations.py
region_mapping_other_parcellations.py
 
 
reunify_both_regions.py
reunify_both_regions.py
 
 
rh_ref_table.txt
rh_ref_table.txt
 
 
subparcel.m
subparcel.m
 
 
subparcel.prj
subparcel.prj
 
 
subparcel_original_ref.m
subparcel_original_ref.m
 
 
transform_mesh_high.py
transform_mesh_high.py
 
 
txt2off.py
txt2off.py
 
 
verif.py
verif.py
 
 

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Surface and Connectivity Reconstruction: Imaging Pipeline for TVB Simulations

SCRIPTS 0.3

Please see the wiki

NEW in 0.3:

  • mrtrix 3.0 RC2
  • many processing/tractography improvements, including new registrations methods, SIFT2, denoise, topup/eddy, bias field corrections, mask upsampling and dilatation, multi-shell multi-tissue, dhollander, better subcortical structure parcellation, tractogram and tdi generation
  • code consolidation, automatic config checks
  • handle automatically reverse phase-encoding DWI in most cases
  • region mapping for subparcellations
  • python 3.5

License

This poject use the MIT License. The full license is in LICENSE.txt in the SCRIPTS distribution.

Copyright (c) [2014] [The SCRIPTS Developers]

How to cite

When citing SCRIPTS, please cite this work:

Proix T, Spiegler A, Schirner M, Rothmeier S, Ritter P, Jirsa, VK. How do parcellation size and short-range connectivity affect dynamics in large-scale brain network models? NeuroImage, 2016, 142:135-149

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prepare data for TVB

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