MRI Processing Pipelines for PAN Healthy Minds for Life Study
Project description
PANpipelines
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
.
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