Running parts of the pipeline

Fetpype comes with three main scripts, located in the workflows folder, than can be called from command line after installing fetpype.

Command	Python script	Description	Input
fetpype_run	pipeline_fet.py	Run the entire fetpype pipeline: pre-processing, reconstruction and segmentation	T2-weighted stacks
fetpype_run_rec	pipeline_rec.py	Run the pre-processing and reconstruction pipeline	T2-weighted stacks
fetpype_run_seg	pipeline_rec.py	Run the segmentation pipeline	Super-resolution reconstructed volume

Note

We recommend you to start by running the entire pipeline with default parameters on a few subjects, to see how the outputs will be structured. This will be useful in particular when running only the segmentation pipeline (fetpype_run_seg), as your data need to be properly formatted for the script to work as expected. More information on output formatting is available here.

Note

Recall that Docker (or Singularity) should be installed and actively running before executing any pipeline command. See the Docker installation guide for your platform. You can verify that Docker is running with docker info.