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7t-mri-pipeline-hpc

Readthedocs compatible

7t_dwi_denoising

Testing compute performance and comparing denoising methods for 7 Tesla Diffusion Weighted Imaging

brainspace

BrainSpace is an open-access toolbox that allows for the identification and analysis of gradients from neuroimaging and connectomics datasets | available in both Python and Matlab |

containers_demo

Demo for containerizing applications with Docker and Singularity

dipy

DIPY is the paragon 3D/4D+ imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

fastsurfer

PyTorch implementation of FastSurferCNN

fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

fs-data-utils

Shell and python utilities for gathering Freesurfer stats into csv format

lesion-mapper

Automated mapping of T2 white matter hyperintensities using FSL

mappertrac

Massively Parallel, Portable, and Reproducible Tractography (MaPPeRTrac). A probabilistic diffusion MRI tractography pipeline for high performance computing. Generates edge-centric connectomes and edge density images. Highly extensible.

micaopen

Open Scripts and pipelines from the Multimodal Imaging and Connectome Analysis Lab at the Montreal Neurological Institute

mrfil.github.io

GitHub Pages for MRFIL Lab

nipype

Workflows and interfaces for neuroimaging packages

pepolar-fmap-intendedfor-populate

persim-rips-singularity

Example code for generating Vietoris-Rips complex persistent homology plots from resting-state functional connectivity NxN Pearson correlation matrices

pydeface

defacing utility for MRI images

qsiprep

Preprocessing and reconstruction of diffusion MRI

qsm_method_comparison_report

BIDS-compatible quantitative susceptibility mapping report generation to compare SWI sequences

rsp

modified Duke BIAC resting-state fc pipeline with SUIT parcellations added

sf_predict

smriprep

Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)