This repository contains a package of scripts and codes used in the paper to convert raw functional images to connectivity matrices using fMRIPrep (https://fmriprep.org/en/stable/)
- A sample TaoWu subject can be accessed here: https://figshare.com/s/dfadce2aaf5d0d94d403?file=36742629
- The fMRIPrep outputs of the same subject fully preprocessed can be accessed here: https://figshare.com/s/dfadce2aaf5d0d94d403?file=36742644
- The set of connectivity matrices (using correlation) generated for the same subject can be accessed here: https://figshare.com/s/dfadce2aaf5d0d94d403?file=36742722
- Containerized execution environment:
- Docker (https://www.nipreps.org/apps/docker/) or
- Singularity (https://www.nipreps.org/apps/singularity/)
- fMRIPrep (version 20.2.3 - https://fmriprep.org/en/stable/index.html)
- dcm2niix (https://github.com/rordenlab/dcm2niix)
- nilearn (https://nilearn.github.io/stable/index.html)
- Install numpy, os, shutil, glob, dcm2niix, nilearn, scipy modules for python programming
- Install Docker/Singularity and fMRIPrep
- Installing fMRIPrep requires several steps and sorting out dependencies and a freesurfer license (free to acquire). We recommend following this guide (https://andysbrainbook.readthedocs.io/en/latest/OpenScience/OS/fMRIPrep.html)
Access Link for Neurocon and TaoWu Dataset : http://fcon_1000.projects.nitrc.org/indi/retro/parkinsons.html A sample TaoWu subject can be accessed here: https://figshare.com/s/dfadce2aaf5d0d94d403?file=36742629
Access Link for ABIDE/ADNI/PPMI : https://ida.loni.usc.edu/login.jsp.
- Each fMRI image needs to be accompanied with a structural T1-weighted (T1w) image acquired from the same subject (ideally) in the same scan session
Raw T1w/fMRI data are in DICOM or NifTi format
- This step is to convert raw MRI data in either DICOM or NifTi into BIDS format (https://bids.neuroimaging.io/)
- ABIDE_Nifti2BIDS.py - To convert raw MRI data (NifTi format) to BIDS - For ABIDE dataset
- ADNI_PPMI_DCM2BIDS.py - To convert raw MRI data (DICOM format) to BIDS - For PPMI and ADNI dataset
- Neurocon and TaoWu dataset are NifTi files and are already BIDS formatted
Make sure you have installed fMRIPrep correctly using the information and guides from the links above.
- Preprocess BIDS formatted neuroimages (1 T1w image and 1 fMRI BOLD image) using fMRIPrep
- fmriprep_shellscript.sh - Script to execute fmriprep preprocessing
- fMRIPrep outputs a number of BIDS Derivative compliant files
- For details on each file: https://fmriprep.org/en/stable/outputs.html
A sample of a fully preprocessed TaoWu subject (and its outputs) can be accessed here: https://figshare.com/s/dfadce2aaf5d0d94d403?file=36742644
Steps D, E, and F: Parcellation and ROI Definition, Connectivity Matrix Extraction, and Graphical Brain Network
- Convert preprocessed Nifti images into connectivity matrices
- ConnectivityMatrices.py - Code to generate connectivity matrices
- The codes we used to run our empirical analysis
- NIPS_paper_gridsearch_experiments.py
- EdgeWeightsStatistics.py
Note: Input/Output location and the required modification are detailed within the python codes