moekay / ATPP_CLI

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

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ATPP command line version

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:

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• 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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