pipetography 0.2.8

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 (recommended):

• To build sandbox singularity image: singularity build -s pipetography.simg singularity.def

• Run singularity image with: singularity run -B <BIDS_DIR>:<Singularity_BIDS_DIR> pipetography.simg (You will have to bind your data directories in addition to just singularity run)

Docker:

• Pull the docker image: docker pull axiezai/pipetography

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

Known container issues:

• The freesurfer license.txt file, although copied into the containers and the environment variable FS_LICENSE is set, must be moved into the freesurfer home folder before running the pipeline. So once your image is built, run it interactively and manually move the license file with mv /license.txt /opt/freesurfer-6.0.0-min/ **Added a move license command in container recipe files'

• 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.

• Containers missing standard libraries like libopenblas or libfortran, this is because $LS_LIBRARY_PATH is missing conda environment's lib path. We need to append the environment's lib path with export LB_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/miniconda-latest/envs/tracts/lib/. The conda env path has been appended as part of the container recipe file

• Freesurfer6.0.0-min recon-all is missing commands if -parallel or -openmp are set to True. The default -parallel setting has been set to False for pipetography.pipeline.

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:

The following pipeline is produced by running the default set up in pipeline. And each individual node in the workflow is shown in core.

#example
from IPython.display import Image
Image('docs/images/output_5_0.png')