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

ATPP command line version

DOI

ATPP (Automatic Tractography-based Parcellation Pipeline)

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

Notice

  • Usage: bash ATPP.sh batch_list.txt

Prerequisites:

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

  • Tools:
    • FSL (with FDT toolbox), SGE and MATLAB (with SPM8)
  • 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 

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

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ATPP (Automatic Tractography-based Parcellation Pipeline) command line version

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