Surface and Connectivity Reconstruction: Imaging Pipeline for TVB Simulations

SCRIPTS 0.4

Please see the wiki

NEW in 0.4:

• Dockerfile for easy installation with Docker.
• Tests.
• Reorganization and simplification of the code => compatibility with tvb-make.
• 4 new parcellations: Destrieux, HCP-MMP1, Yeo7 and Yeo 17.

Features

• prepare data for TVB: surface reconstruction, region mapping, connectome.
• mrtrix 3.0 RC2: SIFT/SIFT2, ACT, 3 types of registration structural/diffusion, denoising, topup/eddy corrections, bias field corrections, mask upsampling and dilatation, multi-shell multi-tissue, dhollander algo, fsl subcortical structure parcellation, tractogram and tdi generation, multi-threaded.
• automatic config checks.
• convenience script for HCP datasets.
• handle automatically reverse phase-encoding DWI in most cases.
• subparcellation in any number of regions along with corresponding region mapping.
• MNE forward model.
• 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