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Surface and Connectivity Reconstruction:

Imaging Pipeline for TVB Simulations - SCRIPTS 0.4.1

Introduction

This pipeline uses T1 and diffusion MRI data to prepare surface, region mapping and connectivity for TVB simulatons in the following way:

• The surface is built with freesurfer
• The region mapping is built from the parcellation of freesurfer on a decimated surface (20.000 vertices)
• The connectivity and length matrices are build with MRtrix using spherical deconvolution and probabilistic tractrography.

Versions of the needed softwares

The pipeline was tested on a Debian wheezy 64 bits

• Freesurfer: tested with freesurfer-x86_64-redhat-linux-gnu-stable5-20130513
• Python: tested with python 2.7.3
• MRtrix: tested with MRtrix 3
• FSL: tested with FSL 5.0
• MNE: tested with MNE 2.7.0

Installation

Please see installation steps

Run the pipeline

• Create a main directory, all data and processed data files will be in this main directory In this main directory you must have:

if using your own data

• a "data" directory with:
  • a "T1" directory with T1 MRI in the nifti or dicom format.
  • a "DWI" directory with dMRI data in nifti or dicom format. If in the nifti format, the bvecs and bvals files must be provided as well in the FSL format; see Mrtrix documentation)

if using HCP data

• a "data" directory with:
  • 100307_3T_Diffusion_preproc.zip
  • 100307_3T_Structural_preproc.zip
  • 100307_3T_Structural_preproc_extended.zip

in both cases

• Clone this repository wherever you want, copy the example_config.sh file (you can copy it to your main directory) and edit it as needed.

• To run the surface pipeline, in a terminal:

cd path_to_scripts
bash main_surface.sh -c path_to_config/config.sh

Troubleshootings

Please check first the FAQ page and the issues to see if the bug is known. Otherwise you can submit a new issue.