pipetography 0.3.3

Pre/Post-processing pipeline for tractography wrapped around nipype and mrtrix3

Pipetography

Nipype and mrtrix3 based pre-/post- processing pipeline for brain diffusion-MRI and generation of structural connectomes of the brain.

This repo currently only has pre-processing capabilities! More will be added in the near future.

The pre-processing workflow has been updated to reflect what's seen in the optimal DESIGNER pipeline and on mrtrix3 cloud apps on brainlife.io.

Install

Since most usages will be on HPC resources, I highly recommend that you use the Singularity or Docker recipe in the repository instead of installing the Python module.

Singularity:

• Currently has pathing issues as seen in the singularity issues page: https://github.com/hpcng/singularity/issues/5040, the 3.6 release candidate should fix this... For now, use docker image if you can. If not, the singularity container will not be able to execute freesurfer recon-all step of the workflow. All DWI preprocessing steps will work though.

• This is a large image, you will need to set the following environment variables to somewhere other than /tmp:

  • export SINGULARITY_TMPDIR={YOUR DESTINATION DIR}
  • export SINGULARITY_LOCALCACHEDIR={YOUR DESTINATION DIR}
  • export SINGULARITY_CACHEDIR={YOUR DESTINATION DIR}
  • export SINGULARITY_PULLFOLDER={YOUR DESTINATION DIR}

• Obtain the singularity image with singularity pull docker://axiezai/pipetography:0.3.2.

• Run interactively with singularity shell --nv --B <BIDS_DIR>:<SINGULARITY_BIDS_DIR> {Path to singularity .sif}

Docker:

• Pull the docker image: docker pull axiezai/pipetography:0.3.2

• Run with BIDS directory and interactive bash terminal: docker run -v <BIDS_DIR>:<Docker_BIDS_DIR> -it axiezai/pipetography:0.3.2 bash

Known container issues:

• Singularity image missing freesurfer path to nu_correct as part of $PATH.

• If singularity build fails with apt-get install error complaining about unauthenticated packages, add --allow-unauthenticated to every apt-get line in the sinngularity.def file.

Creating your own environment and install pipetography as a Python module:

pip install pipetography

Since pipetography is a Nipype wrapper around mrtrix3, ANTs, and FSL, you have to follow their installation instructions and set them up appropriately on your machine as well:

• mrtrix3 v3.0.0

• ANTs

• FSL

• Freesurfer v6.0

• Matlab Run Time Compiler for freesurfer

The pipeline:

Currently supports acquisitions with no reverse phase encoding (-rpe_none) and reverse phase encoding in all DWI directions (-rpe_all) options.