p3 - fmri processing pipeline

p3 is an extensible preprocessing pipeline that encourages experimentation and customization. In addition to providing a BIDS-compatible preprocessing pipeline for users, it also provides a platform to quickly and easily integrate new processing methods into an neuroimaging processing stream.

Powered by the nipype project, p3 takes advantage of the cross package python interface it provides, allowing users to use a variety of neuroimaging software in their pipelines from one standard interface. The nipype concepts of nodes and workflows allows users to construct processing streams in an intuitive manner.

• Installation
  • Docker/Singularity
  • Native Install (For Advanced Users and Developers)
• Usage
  • Overview
  • Running the pipeline
  • Settings
  • Creating workflows and testing
  • Filtering the dataset
• Defaults
  • Settings
  • Outputs
  • Workflows
• Tutorials
  • Example
  • Creating New Workflows
  • Sideloading

Quick Usage

p3 uses the standard BIDS app run command. You can run p3 by simply running:

p3proc [BIDS directory] [output directory]

This will run the p3 pipeline with the all standard built in settings.

If you are using the Docker version of p3, the command is:

docker run -it --rm \
    -v [BIDS directory]:/dataset \
    -v [output directory]:/output \
    p3proc/p3 /dataset /output

where [BIDS directory] and [output directory] are paths on the host system to the BIDS dataset and output directory respectively.

If you are using the Singularity version of p3, the command is:

singularity run \
    -B [BIDS directory]:/dataset \
    -B [output directory]:/output \
    p3proc_p3.simg /dataset /output

where p3proc_p3.simg is replaced with the singularity image filename.