panpipelines 0.9.1

MRI Processing Pipelines for PAN Healthy Minds for Life Study

PANpipelines

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This repository contains all the necessary scripts for reproducing the steps taken to preprocess and analyze MRI data collected during the Precision Aging Network (PAN) project.

The panpipelines package

The PAN Pipelines use a set of python modules packaged under the main panpipelines package to run all the preprocessing and analysis workflows which are based on NiPype.

Installation

It is recommended that a python environment manager like conda or virtualenv is used to install the panpipelines package. Assuming you have created a conda environment called panpython then the package can be installed as follows:

conda activate panpython
pip install panpipelines

Deployment

For an example of using the package to process MRI data please refer to the ./deployment folder. All the necessary parameters for running the pipelines are described in a config file in the ./config subdirectory which is passed as a parameter to the main module pan_processing.py. In the example provided this file is name panpipeconfig_slurm.config.