Lead-DBS User Guide
  • Introduction
  • How to contribute to Lead-DBS
  • Installation
  • Lead-DBS
    • Overview
    • Self-Tutoring with Lead-Tutor
    • 1. Load Patient Folder
      • Importing a classic Lead-DBS dataset to BIDS version
    • 2. Image Import
      • Converting NIfTI-images into BIDS
      • Converting DICOM files into BIDS
    • 3. Volume Registrations
      • Coregister Volumes
      • Normalizing the Images
      • Brainshift Correction
      • Checking the Coregistration and Normalization
    • 4. (optional) Surface Reconstruction
    • 5. (optional) Reconstruction of Electrode Trajectories
      • Orientation of Directional Leads
        • Prerequisites
        • Automatic Algorithm
        • Possible Problems with the Automatic Algorithm
        • User-Assisted Algorithm (Manual Refine)
      • TRAC/CORE Details
      • Manual Reconstruction
      • Reconstruction File
    • 6. (optional) Perform Connectivity Analysis
    • 7. Visualization
      • MER Analysis
    • Reconstruction Statistics
  • Lead-Group
    • Group analyses with Lead-DBS
    • Setup Analysis
    • General Settings
    • Group Visualization
    • Calculate VTA and Stats
    • Sweetspot Explorer
  • Connectomics
    • Connectomics
      • Diffusion MRI: Patient Specific Processing
      • fMRI-Analysis: Patient Specific Processing
      • Using Normative Connectomes
      • Network Mapping Explorer
      • Fiber Filtering Explorer
    • Lead Connectome Mapper
  • Lead-OR
    • Imaging setup
    • Electrophysiology setup
    • Using the platform
  • Appendix
    • Code Backbone
    • Acquiring and Installing Atlases
      • Customizing Atlas Visualization
    • Troubleshooting / Specific Help
      • Adding Fortran dependencies for VTA modeling
      • VTA Calculation Troubleshoot
    • Command line interface
      • Command line options
    • Matlab scripting examples
      • Installing an atlas from an online repository
      • Warping a normative connectome to native subject space
    • Using Slicer
      • Sweet-sour spot
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  • On a Mac
  • For Windows
  1. Appendix
  2. Troubleshooting / Specific Help

Adding Fortran dependencies for VTA modeling

PreviousTroubleshooting / Specific HelpNextVTA Calculation Troubleshoot

Last updated 3 years ago

The FEM-based VTA model (Horn et al. 2017) needs Fortran dependencies since it uses the that is partially based on Fortran code.

On a Mac

  1. Open a Terminal

  2. If you don't have home-brew installed, do so by typing

    /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

  3. Install gcc by typing brew install gcc

  4. Add a symbolic link between the file libgfortran.3.dylib to /usr/local/lib/ folder. You can do so by e.g. typing

    ln /usr/local/Cellar/gcc@4.9/4.9.4/lib/gcc/4.9/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib

    into the Terminal. However, depending on the installation of your local gcc, folders might be a bit different in your case.

For Windows

Check if you have the "Intel(R) Visual Fortran Redistributables for Windows" installed on your system. Otherwise they can be found here:

If you do not have them already you might also need "MicrosoftVisual c++ 2008 Redistributables" as well as a C++ compiler. In our experience the model works when you have c++ 2008 Redistributables version 9.0.30729.6161 and version 9.0.21022 installed. If you experience problems when trying to run the model we recommend to install these versions.

SimBio toolbox
https://software.intel.com/en-us/articles/redistributable-libraries-of-the-intel-c-and-fortran-compiler-for-windows/