https://github.com/lren-chuv/mri-parallel-nmm-pipeline
Wrapper to run the SPM12 neuromorphometric pipeline in parallel over multiple CPU cores
https://github.com/lren-chuv/mri-parallel-nmm-pipeline
data-factory
Last synced: 7 months ago
JSON representation
Wrapper to run the SPM12 neuromorphometric pipeline in parallel over multiple CPU cores
- Host: GitHub
- URL: https://github.com/lren-chuv/mri-parallel-nmm-pipeline
- Owner: LREN-CHUV
- Created: 2019-07-19T12:50:32.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-01-10T14:45:48.000Z (almost 6 years ago)
- Last Synced: 2025-01-19T15:34:54.432Z (9 months ago)
- Topics: data-factory
- Language: Python
- Size: 10.7 KB
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# MRI parallel neuromorphometric pipeline
## Introduction
The MRI parallel neuromorphometric pipeline is a wrapper to run the SPM12 neuromorphometric pipeline in parallel over multiple CPU cores.
## Prerequisites
* Python 3.6 (see: https://www.python.org/)
* Matlab (see: https://ch.mathworks.com/products/matlab.html)
* SPM12 deployed in /opt folder (see: https://www.fil.ion.ucl.ac.uk/spm/software/spm12/)
* Matalb engine for Python must be installed (see: https://www.mathworks.com/help/matlab/matlab_external/install-the-matlab-engine-for-python.html)
* The input folder must contain nifti files organized according to the following directory tree: subject/visit/protocol/repetition/ (see: https://github.com/HBPMedical/nmm-pipeline-nifti-organizer)
* If the protocol as per previous bullet-point is not T1, you'll have to update the protocol definition file from the mri-preprocessing-pipeline subproject (see: https://github.com/HBPMedical/mri-preprocessing-pipeline)
## Installation
Run: `git clone --recursive https://github.com/HBPMedical/mri-parallel-nmm-pipeline.git` (or download the zipped source code at: https://github.com/HBPMedical/mri-parallel-nmm-pipeline/archive/master.zip and retreive the git submodule if needed)
## Usage
Run (from the project directory): `./mri_parallel_preprocessing.py `
## LICENSE & COPYRIGHT
This project makes use of another project, referenced as a Git submodule.
Please look at that submodule repository for its license, its copyright and further information.