Pre/Post-processing pipeline for tractography wrapped around nipype and mrtrix3
Project description
Pipetography
Nipype and mrtrix3 based pre-/post- processing pipeline for brain diffusion-MRI and generation of structural connectomes of the brain.
The pre-processing pipeline has been updated to reflect what's seen in the optimal DESIGNER pipeline and on mrtrix3 cloud apps on brainlife.io.
The post-processing pipeline, including co-registration of atlases and connectome generation is now included in the connectomes module
Install
Since most usages will be on HPC resources, I highly recommend that you use the Singularity
definition file in the repository instead of installing the Python module.
Singularity:
-
This is a large image, you will need to set the following environment variables to somewhere other than
/tmp
if you want to avoid memory errors:export SINGULARITY_TMPDIR={YOUR DESTINATION DIR}
export SINGULARITY_LOCALCACHEDIR={YOUR DESTINATION DIR}
export SINGULARITY_CACHEDIR={YOUR DESTINATION DIR}
export SINGULARITY_PULLFOLDER={YOUR DESTINATION DIR}
-
Build the singularity image with the
singularity.def
file provided in Github, you will need to havesudo
permissions to perform singularity build. If you run into memory problems, consider building as a sandbox at first with the-s
flag.sudo singularity build {image_file_name}.sif singularity.def
-
OR pull the built singularity image from cloud library:
singularity pull --arch amd64 library://axiezai/pipetography/pipetography:latest
Docker:
- Docker often encounters permission problems on HPC resources, using the docker container is only recommended if you have
sudo
permissions to the machine. - Use the
Dockerfile
in this repo to build your own Docker container.
Usage:
- To run the singularity container interactively, you will need a few flags:
-e
flag for a clean environnment upon container start-B
flag to bind your BIDS directory into the container.
- Example:
singularity shell -e -B <BIDS_DIR>:<SINGULARITY_BIDS_DIR> {Path to singularity .sif}
will start an interactive shell.singualrity exec -e -B <BIDS_DIR>:<SINGULARITY_BIDS_DIR> {Path to singularity .sif} python dwi_pipeline.py
will execute the input python code. See pipeline for an example python script that preprocesses BIDS DWI data.
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:
Everything listed in this section is included in the Singularity and Docker containers.
The pipeline:
Currently supports acquisitions with no reverse phase encoding (-rpe_none
) and reverse phase encoding in all DWI directions (-rpe_all
) options. See pipeline for preprocessing details, and connectomes for postprocessing details.
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