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+# HCP Pipeline for Diffusion Processing
+
+This is a Python implementation of the Diffusion Preprocessing procedure in 
+[HCP Pipeline](https://github.com/Washington-University/HCPpipelines.git). Similar to the original 
+implementation, the input data need to be organised with HCP-like folder structure.
+
+## Prerequisite
+
+The pipeline requires 3 softwares: FSL, FreeSurfer, and Connectome Workbench. To use containerised 
+versions, the absolute path to the Singularity images can be passed with the `--fsl_simg`, 
+`--fs_simg`, and `--wb_simg` flags respectively.
+
+## Usage
+
+```bash
+hcpdiffpy --help
+
+usage: hcpdiffpy [-h] [--workdir WORK_DIR] [--output_dir OUTPUT_DIR] [--fsl_simg FSL_SIMG]
+                 [--fs_simg FS_SIMG] [--wb_simg WB_SIMG] [--condordag]
+                 subject_dir subject ndirs [ndirs ...] phases [phases ...] echo_spacing
+
+HCP Pipeline for diffusion preprocessing
+
+positional arguments:
+  subject_dir           Absolute path to the subject's data folder (organised in HCP-like structure)
+  subject               Subject ID
+  ndirs                 List of numbers of directions
+  phases                List of 2 phase encoding directions
+  echo_spacing          Echo spacing used for acquisition in ms
+
+options:
+  -h, --help            show this help message and exit
+  --workdir WORK_DIR    Absolute path to work directory (default: /data/project/hcpa_dwi_proc)
+  --output_dir OUTPUT_DIR
+                        Absolute path to output directory (default: /data/project/hcpa_dwi_proc)
+  --fsl_simg FSL_SIMG   singularity image to use for command line functions from FSL (default: None)
+  --fs_simg FS_SIMG     singularity image to use for command line functions from FreeSurfer
+                        (default: None)
+  --wb_simg WB_SIMG     singularity image to use for command line functions from Connectome
+                        Workbench (default: None)
+  --condordag           Submit workflow as DAG to HTCondor (default: False)
+```
+
+# References
+Glasser, M.F., et al. 2013. The minimal preprocessing pipelines for the Human Connectome Project. 
+*NeuroImage*, 80:105-24. 
+DOI: [10.1016/j.neuroimage.2013.04.127](https://doi.org/10.1016/j.neuroimage.2013.04.127)