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@CoBrALab Computational Brain Anatomy Laboratory

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    52 repositories

    • documentation

      Public
      Documentation for every thing, everything documented
      6•43•2•0•Updated Jan 5, 2026Jan 5, 2026

    • RABIES

      Public
      fMRI preprocessing pipeline and analysis tools adapted for rodent images. Visit the full documentation at https://rabies.readthedocs.io/
      Python
      •
      Other
      •22•48•49•6•Updated Dec 23, 2025Dec 23, 2025

    • simpleitk_timeseries_motion_correction

      Public
      Python
      •1•1•10•1•Updated Dec 17, 2025Dec 17, 2025

    • ODC-Mouse-Forms

      Public
      A repo containing OpenDataCapture forms for tracking mouse data gathered from experiments within the CoBra Lab
      TypeScript
      •1•1•17•4•Updated Dec 16, 2025Dec 16, 2025

    • antsRegistration_affine_SyN

      Public
      Shell
      •0•2•2•0•Updated Dec 12, 2025Dec 12, 2025

    • synthstrip_N3

      Public
      A preprocessing tool for human T1w MRIs
      Shell
      •1•2•6•0•Updated Nov 27, 2025Nov 27, 2025

    • cobralib

      Public
      Utility and helper scripts
      Shell
      •0•0•0•0•Updated Nov 26, 2025Nov 26, 2025

    • MAGeTBrain-nextflow

      Public
      Nextflow
      •
      Other
      •0•0•13•0•Updated Nov 19, 2025Nov 19, 2025

    • iterativeN3

      Public
      Shell
      •
      Other
      •0•0•8•0•Updated Nov 12, 2025Nov 12, 2025

    • iterativeN4_multispectral

      Public
      A pipeline which performs iterative classification and bias field correction of T1-weighted MRIs
      Shell
      •
      Other
      •1•1•10•0•Updated Nov 12, 2025Nov 12, 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 Nov 12, 2025Nov 12, 2025

    • preclinical_N3

      Public
      Shell
      •0•1•4•0•Updated Nov 10, 2025Nov 10, 2025

    • optimized_antsMultivariateTemplateConstruction

      Public
      A re-implementation of antsMultivariateTemplateConstruction2.sh using optimized image pyramid scale-space and qbatch support
      Shell
      •
      Other
      •11•35•38•1•Updated Nov 10, 2025Nov 10, 2025

    • CPCA

      Public
      Complementary principal component analysis (CPCA) for fMRI confound correction.
      Python
      •0•0•0•0•Updated Nov 4, 2025Nov 4, 2025

    • minc-toolkit-extras

      Public
      Extra miscellaneous scripts for minc-toolkit
      Shell
      •
      Other
      •7•8•8•1•Updated Oct 20, 2025Oct 20, 2025

    • libBIDS.sh

      Public
      Shell
      •
      MIT License
      •3•21•6•1•Updated Oct 6, 2025Oct 6, 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

    • 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 archive
      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

    • 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

    • 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