fmri-preprocessing-pipeline

A comprehensive fMRI preprocessing pipeline with distortion correction, motion correction, denoising, and connectome matrix construction

https://github.com/lucsam/fmri-preprocessing-pipeline

Science Score: 44.0%

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Repository

A comprehensive fMRI preprocessing pipeline with distortion correction, motion correction, denoising, and connectome matrix construction

Basic Info

Host: GitHub
Owner: LucSam
License: mit
Language: Shell
Default Branch: main
Size: 3.12 MB

Statistics

Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 0

Created 12 months ago · Last pushed 10 months ago

Metadata Files

Readme License Citation

fMRI Preprocessing Pipeline

A comprehensive fMRI preprocessing pipeline with distortion correction, motion correction, advanced denoising techniques (ICA-AROMA and CompCor), and functional connectivity matrix construction, making it suitable for both clinical and research applications.

Features

DICOM to NIfTI conversion using MRtrix3
Distortion correction using FSL's TOPUP
Motion correction using FSL's MCFLIRT
Brain extraction using ANTsPyNet
T1 to fMRI registration using ANTs
Tissue segmentation using choice of ANTs Deep Atropos or FreeSurfer SynthSeg
Atlas registration with support for AAL, Schaefer, and FreeSurfer parcellations
ICA-based denoising with MELODIC and ICA-AROMA
CompCor denoising with optional bandpass filtering
Functional connectivity matrix creation
Extensive quality control visualizations
Detailed HTML and text summary reports

Documentation

For detailed documentation, please see documentation.

Usage

```bash ./fmri-preprocessing-pipeline-10.sh -s /path/to/subject \ -d "010SpinEchoFieldMapAP,011SpinEchoFieldMapPA,012rfMRIRESTAP,013rfMRIREST_AP" \ -A aal -a /path/to/AAL.nii \ -t /path/to/t1.nii.gz \ -S atropos \ -I /path/to/ICA-AROMA.py \ -C 1 -N 5 -B 1 -L 0.08 -H 0.01

Owner

Name: Lucius
Login: LucSam
Kind: user

Twitter: LuciusFekonja
Repositories: 1
Profile: https://github.com/LucSam

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: "Fekonja"
    given-names: "Lucius"
  - family-names: "Karatay"
    given-names: "Onurhan"
title: "fMRI Preprocessing Pipeline"
version: 1.0.0
date-released: 2025-03-14
url: "https://github.com/LucSam/fmri-preprocessing-pipeline"

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