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

ATPP (Automatic Tractography-based Parcellation Pipeline)

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

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 &
   

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

• 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 

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