Repositories list

• ODC-Mouse-Forms

  Public
  A repo containing OpenDataCapture forms for tracking mouse data gathered from experiments within the CoBra Lab

  TypeScript

  •1•1•9•0•Updated Oct 16, 2025Oct 16, 2025

• RABIES

  Public
  fMRI preprocessing pipeline and analysis tools adapted for rodent images. Visit the full documentation at https://rabies.readthedocs.io/

  Python

  •

  Other

  •22•46•61•8•Updated Oct 10, 2025Oct 10, 2025

• libBIDS.sh

  Public
  Shell

  •

  MIT License

  •1•20•6•0•Updated Oct 6, 2025Oct 6, 2025

• MAGeTBrain-nextflow

  Public
  Nextflow

  •

  Other

  •0•0•13•0•Updated Sep 29, 2025Sep 29, 2025

• synthstrip_N3

  Public
  A preprocessing tool for human T1w MRIs

  Shell

  •0•2•3•0•Updated Sep 22, 2025Sep 22, 2025

• optimized_antsMultivariateTemplateConstruction

  Public
  A re-implementation of antsMultivariateTemplateConstruction2.sh using optimized image pyramid scale-space and qbatch support

  Shell

  •

  Other

  •10•32•36•1•Updated Sep 19, 2025Sep 19, 2025

• WMH_UKB_menopause

  Public
  WMH_UKB_menopause

  R

  •0•0•0•0•Updated Sep 2, 2025Sep 2, 2025

• qbatch

  Public
  Python

  •

  The Unlicense

  •13•33•28•2•Updated Aug 16, 2025Aug 16, 2025

• make_slice_images

  Public
  Shell

  •0•2•4•0•Updated Aug 8, 2025Aug 8, 2025

• minc-toolkit-extras

  Public
  Extra miscellaneous scripts for minc-toolkit

  Shell

  •

  Other

  •7•8•8•1•Updated Jul 16, 2025Jul 16, 2025

• bids2mnc

  Public
  Script to convert BIDS-structured neuroimaging into a metadata-rich MINC files

  Shell

  •0•1•6•0•Updated Jul 14, 2025Jul 14, 2025

• WMH_patho_UKB

  Public
  R

  •0•1•0•0•Updated Jun 10, 2025Jun 10, 2025

• twolevel_ants_dbm

  Public
  A twolevel deformation based morphometry pipeline using ants

  Python

  •

  Other

  •8•13•19•1•Updated May 16, 2025May 16, 2025

• mousefmri_acq_publication

  Public
  Contains all the code for reproducing analyses and figures in the mouse fmri acquisition guidelines paper

  Jupyter Notebook

  •0•2•0•0•Updated May 10, 2025May 10, 2025

• CobraLab.github.io

  Public
  Website

  HTML

  •

  Other

  •4k•0•6•0•Updated Mar 4, 2025Mar 4, 2025

• CPCA

  Public
  Complementary principal component analysis (CPCA) for fMRI confound correction.

  0•0•0•0•Updated Feb 5, 2025Feb 5, 2025

• minc-bpipe-library

  Public
  Library of bpipe implemented commands commonly applied to minc datafiles, suitable for importing into other pipelines

  Shell

  •

  Other

  •8•13•10•1•Updated Jun 21, 2024Jun 21, 2024

• MAGeTbrain

  Public
  Multiple Automatically Generated Templates brain segmentation algorithm

  Python

  •

  Other

  •24•50•12•0•Updated Jun 18, 2024Jun 18, 2024

• HitchhikersGuideToNeuroimaging

  Public
  The Hitchhiker's Guide To Neuroimaging - All the things HOWTOs don't tell you

  0•1•5•0•Updated May 13, 2024May 13, 2024

• UKBB-tabular-processing

  Public
  Scripts to handle the tabular data associated with the UK BioBank

  Python

  •1•9•7•0•Updated Mar 15, 2024Mar 15, 2024

• RABIES_tutorial

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •3•2•0•0•Updated Mar 12, 2024Mar 12, 2024

• iterativeN3

  Public
  Shell

  •

  Other

  •0•0•8•0•Updated Feb 16, 2024Feb 16, 2024

• WMH_Signal_AD_OParent_2023

  Public
  WMH signal measures paper

  R

  •0•0•0•0•Updated Dec 7, 2023Dec 7, 2023

• MousePhgyMetrics

  Public
  Extracts various instantaneous metrics from the raw respiration and pulse oximetry traces

  Python

  •0•3•0•0•Updated Aug 9, 2023Aug 9, 2023

• QLS-course-materials

  Public
  Materials for the 2022 NeuroDataScience Course (McGill QLSC612)

  Jupyter Notebook

  •23•0•0•0•Updated May 2, 2023May 2, 2023

• cobra-nmf

  Public
  Collection of scripts for formatting vertex and/or voxel data into matrix format

  Python

  •3•5•8•0•Updated Apr 19, 2023Apr 19, 2023

• cortical_markers_paper

  Public
  All code used to generate the results seen in the manuscript ____

  MATLAB

  •0•0•0•0•Updated Mar 13, 2023Mar 13, 2023

• antsRegistration-MAGeT

  Public
  A reimplementation of MAGeTbrain using only ANTs tools.

  Shell

  •

  Other

  •6•16•20•1•Updated Jan 5, 2023Jan 5, 2023

• design-choices-cca-neuroimaging

  Public
  Python

  •0•0•0•0•Updated Dec 13, 2022Dec 13, 2022

• fMRI_phantom_analysis

  Public
  Python

  •1•4•0•0•Updated Nov 21, 2022Nov 21, 2022