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          _     _________  _______  _______
         / \   |  _   _  ||_   __ \|_   __ \
        / _ \  |_/ | | \_|  | |__) | | |__) |
       / ___ \     | |      |  ___/  |  ___/
     _/ /   \ \_  _| |_    _| |_    _| |_
    |____| |____||_____|  |_____|  |_____|

ATPP GUI version

DOI

ATPP (Automatic Tractography-based Parcellation Pipeline)

  • Single-ROI oriented brain parcellation
  • Automatic parallel computing
  • Modular and flexible structure
  • Simple and easy-to-use settings

Installation

  1. Install build tools.

    For RedHat/CentOS:

    sudo yum groupinstall 'Development Tools'
    sudo yum groupinstall 'Desktop Platform Development'

    For Debian/Ubuntu/Mint:

    sudo apt-get install build-essential
  2. Install GTK2 backend:

    For RedHat/CentOS:

    sudo yum install gtk2-devel libglade2-devel

    For Debian/Ubuntu/Mint:

    sudo apt-get install libgtk2.0-dev libglade2-dev
  3. Install gedit

    For RedHat/CentOS:

    sudo yum install gedit

    For Debian/Ubuntu/Mint:

    sudo apt-get install gedit
  4. Install ffcall (already included in the repository):

    git clone https://github.com/haililihai/ATPP_GUI.git
    cd ATPP_GUI/ffcall-1.10
    ./configure; make; sudo make install
  5. Install gtk-server (already included in the repository):

    cd ../gtk-server-2.3.1-sr
    ./configure; make; sudo make install
    cd ..

    In the step of 'make', if the following error arises:

    libdl.so.2: error adding symbols: DSO missing from command line

    Please edit the Makefile in the directory of gtk-server

    cd ../gtk-server-2.3.1-sr
    gedit Makefile
    # add '-ldl' option to the LDFLAGS
    # e.g. LDFLAGS = -ldl ...
    # then make again
    make; sudo make install
  6. Finally, run ATPP:

    ./ATPP &
    

Prerequisites:

===============================================

  • Tools:
    • FSL (with FDT toolbox), SGE and MATLAB (with SPM8), Gedit
    • gtk-server and ffcall libraries, which have been included in this repository
  • Data files:
    • T1 image for each subject
    • b0 image for each subject
    • images preprocessed by FSL(BedpostX) for each subject
  • Directory structure:
     Working_dir
     |-- sub1
     |   |-- T1_sub1.nii
     |   |-- b0_sub1.nii
     |-- ...
     |-- subN
     |   |-- T1_subN.nii
     |   |-- b0_subN.nii
     |-- ROI
     |   |-- ROI_L.nii
     |   `-- ROI_R.nii
     `-- log 

===============================================