Version updated

September 2024 (v0.4): -bigventricles option added
August 2024 (v0.3): -procDir option added & dwi registration command changed (FSL -> ANTs)
June 2024 (v0.2) : GAN-MAT implemented
March 2024 (v0.1) : Initial version released

FuNP

Fusion of Neuroimaging Preprocessing Pipeline: A multimodal MRI data preprocessing pipeline

Paper

B.-y. Park, K. Byeon, and H. Park. FuNP (Fusion of Neuroimaging Preprocessing) pipelines: A fully automated preprocessing software for functional magnetic resonance imaging. Frontiers in Neuroinformatics 13:5 (2019).
https://www.frontiersin.org/articles/10.3389/fninf.2019.00005/full

Required software 👀

Important

The current version of FuNP was tested under the following versions

AFNI v22.0.17 (https://afni.nimh.nih.gov/download)
FSL v6.0 (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation)
FreeSurfer v7.1.1 (http://freesurfer.net/fswiki/DownloadAndInstall)
ANTs v2.3.5 (https://github.com/ANTsX/ANTs)
MRtrix3 v3.0.2 (https://www.mrtrix.org/download)
Workbench v1.5.0 (https://www.humanconnectome.org/software/get-connectome-workbench)
R v3.6.3 (https://cran.r-project.org/bin/linux/ubuntu/fullREADME.html)
python v3.8.5 (https://www.python.org/downloads)
FIX v1.06.15 (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX)

Python3 libraries

• numpy v1.24.3
• scipy v1.13.0
• nibabel v5.2.1
• pygeodesic v0.1.9
• nilearn v0.10.4
• matplotlib v3.8.4
• brainspace v0.1.10
• vtk v9.3.0
• pyvirtualdisplay v3.0
• torch v2.3.1+cu121

🚩 FIX requirements

• FSL
• MATLAB with official toolboxes:
  • Statistics
  • Signal Processing
• R (version >=3.3.0), with the following packages:
  • 'kernlab' version 0.9.24
  • 'ROCR' version 1.0.7
  • 'class' version 7.3.14
  • 'party' version 1.0.25 ('coin' version 1.1.0)
  • 'e1071' version 1.6.7
  • 'randomForest' version 4.6.12

🚩 GAN-MAT requirements

• Download the trained model (model.pth) at https://www.dropbox.com/home/GAN-MAT?di=left_nav_browse
• Locate model.pth into the ~/FuNP/functions/GANMAT folder