Repositories list

• LAMAReg

  Public
  Label based Modality Agnostic Registration (LAMAReg) is a MRI resgistration technique combines deep learning-based segmentation and numerical solutions to generate precise non linear warpfields

  Python

  •

  Other

  •1•5•5•0•Updated Sep 16, 2025Sep 16, 2025

• micaflow

  Public
  The easy way to process MRI data

  pythonmriregistration+ 3neuroimagingniftimri-brain

  Python

  •0•1•1•0•Updated Sep 15, 2025Sep 15, 2025

• z-brains

  Public
  z-brains: open software for brain lesion lateralization and localization

  mrineuroimagingepilepsy+ 3lesionlateralizationze-brain

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •6•11•8•1•Updated Sep 15, 2025Sep 15, 2025

• MICA-7t

  Public
  scripts for 7t sorting and organizing

  Shell

  •

  GNU General Public License v3.0

  •0•8•0•0•Updated Sep 10, 2025Sep 10, 2025

• micapipe

  Public
  micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below

  awesomemrineuroimaging+ 7imageprocessingbidsmicrostructurediffusion-mriconnectomeresting-statemultimodal

  Shell

  •

  GNU General Public License v3.0

  •39•109•28•5•Updated Aug 22, 2025Aug 22, 2025

• MICA-MNI.github.io

  Public
  HTML

  •

  Creative Commons Zero v1.0 Universal

  •0•1•0•0•Updated Jul 28, 2025Jul 28, 2025

• endex-epilepsy.github.io

  Public
  Epilepsy Neuroimaging Data Exchange

  HTML

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Jul 26, 2025Jul 26, 2025

• ENIGMA

  Public
  The ENIGMA Toolbox is an open-source repository for accessing 100+ ENIGMA statistical maps, visualizing cortical and subcortical surface data, and relating neuroimaging findings to micro- and macroscale brain organization. 🤠

  visualizationopen-sourceawesome+ 10multisiteanalysismrienigmaneuroimagingconnectomicsworkflows+ 3

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •42•162•9•0•Updated Jul 14, 2025Jul 14, 2025

• 2025_in-vivo_tauPET-mk6240_TLE

  Public
  This repository provides code for analyzing in-vivo tau aggregation in temporal lobe epilepsy (TLE) using 18F-MK6240 PET. It includes preprocessing, statistical analysis, and visualization scripts to assess tau deposition, connectivity patterns, and cognitive associations in TLE patients and controls.

  Jupyter Notebook

  •

  MIT License

  •0•3•1•0•Updated May 20, 2025May 20, 2025

• Wang_MovieWatching

  Public
  Code for the movie-watching project

  GNU General Public License v3.0

  •0•0•0•0•Updated May 15, 2025May 15, 2025

• MRI-Histology_framework_for_SWM_architecture

  Public
  This repository contains analysis notebooks for studying SWM microstructure using post-mortem and in-vivo datasets. It includes preprocessing, statistical analysis, and visualization scripts to assess intensity profiles from all datasets, gradients from qMRI, and their correlations with cortical geometry, functional and structural connectivity.

  Jupyter Notebook

  •

  MIT License

  •2•3•0•0•Updated May 14, 2025May 14, 2025

• TLE_rsfmri-deviations

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 14, 2025May 14, 2025

• micaopen

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

  machine-learningneuroscienceneuroimaging+ 6networksgradientsconnectomicshistologymultimodalmulti-scale

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •43•80•1•2•Updated May 9, 2025May 9, 2025

• LAMAR-Models

  Public
  Models for LAMAR's synthseg backend

  0•0•0•0•Updated Apr 10, 2025Apr 10, 2025

• GeneticRisk_TLE

  Public
  Structural correlates of epilepsy genetic risk

  Python

  •1•0•0•0•Updated Feb 6, 2025Feb 6, 2025

• BrainSpace

  Public
  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 |

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •80•233•9•4•Updated Feb 6, 2025Feb 6, 2025

• Wang_MultimodalGradient

  Public
  MATLAB

  •

  GNU General Public License v3.0

  •1•2•0•0•Updated Jan 31, 2025Jan 31, 2025

• hippomaps

  Public
  Toolbox and data repository for hippocampal surface data

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •4•3•0•0•Updated Dec 4, 2024Dec 4, 2024

• BrainStat

  Public
  A statistics and context decoding toolbox for neuroimaging.

  pythonstatisticsmatlab+ 1neuroimaging

  Jupyter Notebook

  •

  Other

  •24•109•11•0•Updated Sep 27, 2024Sep 27, 2024

• AllenMouse

  Public
  Expression of genes in hippocampis

  Jupyter Notebook

  •0•0•0•0•Updated May 7, 2024May 7, 2024

• Hippo_Spin_Testing

  Public
  Spin testing implemented in the hippocampus using HippUnfold

  Jupyter Notebook

  •2•0•0•0•Updated Nov 6, 2023Nov 6, 2023

• MICs_tasks

  Public
  Workflow for tasks, from raw files to bids tsv

  R

  •0•0•0•0•Updated Jun 22, 2023Jun 22, 2023

• micapipe-supplementary

  Public
  R

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Jun 15, 2023Jun 15, 2023

• bibliography

  Public
  MICA Bibliography

  TeX

  •

  The Unlicense

  •0•0•0•0•Updated Dec 17, 2021Dec 17, 2021

• 7T-battery

  Public
  7T ‘precision imaging' plan

  Python

  •0•0•0•0•Updated Nov 15, 2021Nov 15, 2021

• NeuroimagingDataScience

  Public
  Neuroimaging Data Science Class NEUR 608

  HTML

  •1•2•0•0•Updated Aug 17, 2020Aug 17, 2020

• surfstat

  Public
  HTML

  •1•0•0•0•Updated Apr 10, 2019Apr 10, 2019

• autism-workshop-2019.github.io

  Public
  CSS

  •0•0•0•0•Updated Dec 14, 2018Dec 14, 2018

• CBIG

  Public
  MATLAB

  •

  MIT License

  •403•0•0•0•Updated Sep 12, 2018Sep 12, 2018

• Presentations

  Public
  1•1•0•0•Updated Jun 12, 2018Jun 12, 2018