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reckbo / dtipipe

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An implementation of PNL's DTI processing scripts and pipelines. Pipelines are implemented using Luigi.

Install

Using Poetry

poetry new my_project
cd my_project
poetry add --git https://github.com/reckbo/dtipipe

Using Pip

If using virtualenv:

virtualenv .venv --python=python3
source .venv/bin/activate{.*sh}

Numpy needs to be installed first otherwise tract_querier fails to build:

pip install numpy
pip install git+https://github.com/reckbo/dtitpipe

Scripts

Script Description
bse Extracts the baseline (B0) from a nifti DWI
eddy_pnl Performs eddy current correction by registering each volume to the first B0
bet_mask Create a mask using FSL's bet
apply_antsRegistrationSyNMI Runs antsRegistrationSyNMI.sh script to compute a transformation and then applies it to the target volume.
fs2dwi Registers Freesurfer labelmap to DWI space.
nifti2nhdr Convert a nifti to nrrd by creating an nhdr header
ukf Run UKFTractography given a DWI and DWI mask in NIFTI format
ukf_tract_querier Wrapper around tract_querier that removes short tracts and converts nan's/inf's to 0's and large numbers

To run a script, simply activate your python environment and call the script, e.g

Using virtualenv:

source .venv/bin/activate{.*sh*}
ukf --help

Using Poetry:

poetry run ukf --help

or

poetry shell
ukf --help

Pipelines

Pipelines are implemented using Luigi, and are saved under src/dtipipe/pipelines.

Here's an example on how to initialize and run a pipeline for a particular session.

First, configure your default parameters and software locations and use those as input to the UKFTracts task, which is the standard_pnl pipeline's final output.

from plumbum import local
from dtipipe.pipeline import standard_pnl

OUTPUT_DIR = local.path(__file__).parent.parent.parent / 'output'

# Parameters
DWI_BET_MASK_THRESHOLD = 0.1

# Software
SOFTWARE = local.path('/cluster/software')
UKFTRACTOGRAPHY_BIN = SOFTWARE / 'UKFTractography-017c06f'
ANTSPATH = SOFTWARE / 'ANTs-build' / 'bin'
FSL_DIR_5_0_7 = local.path('/usr/packages/fsl/5.0.7')
FSL_DIR_6_0_1 = local.path('/usr/packages/fsl/6.0.1')
FREESURFER_HOME_6 = local.path('/usr/local/freesurfer/stable6')

# Control
NUM_PROC_EDDY = 25
NUM_PROC_ANTS = 25
NUM_PROC_ANTS_UKF_TRACT_QUERIER = 25

def make_task(subject_id, session_id, dwi_dicom_dir, freesurfer_recon_dir):
    return UkfTracts(dicom_dir=dwi_dicom_dir,
                     freesurfer_recon_dir=freesurfer_recon_dir,
                     output_session_dir=OUTPUT_DIR / subject_id / session_id
                     output_basename='dwi',
                     dwi_bet_mask_threshold=dwi_bet_mask_threshold,
                     ukf_params={},
                     fsldir=fsldir,
                     antspath=antspath,
                     freesurfer_home=freesurfer_home,
                     ukftractography_bin=UKFTRACTOGRAPHY_BIN,
                     num_proc_eddy=num_proc_eddy,
                     num_proc_ants=num_proc_ants,
                     num_proc_ukf_tract_querier=num_proc_ukf_tract_querier)

Now you can create and run the Luigi task:

import luigi
ukf_tracts_task = make_task('subject_001', 'session_001', '/data/subject_001/session_001/dwi_dicoms/',  
                            '/data/subject_001/session_001/freesurfer_recon')
luigi.build([ukf_tracs_task], workers=1)