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    52 repositories

    • optimized_antsMultivariateTemplateConstruction

      Public
      A re-implementation of antsMultivariateTemplateConstruction2.sh using optimized image pyramid scale-space and qbatch support
      Shell
      •
      Other
      •11•36•39•3•Updated Apr 16, 2026Apr 16, 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•55•55•6•Updated Apr 16, 2026Apr 16, 2026

    • PyQC

      Public
      Python+Qt5 Interface for quickly quality-controlling arbitrary sets of images
      Python
      •
      GNU General Public License v3.0
      •1•2•3•1•Updated Apr 7, 2026Apr 7, 2026

    • ODC-Mouse-Forms

      Public
      A repo containing OpenDataCapture forms for tracking mouse data gathered from experiments within the CoBra Lab
      TypeScript
      •1•2•10•0•Updated Mar 31, 2026Mar 31, 2026

    • libBIDS.sh

      Public
      Shell
      •
      MIT License
      •3•21•7•1•Updated Mar 20, 2026Mar 20, 2026

    • UKBB-tabular-processing

      Public
      Scripts to handle the tabular data associated with the UK BioBank
      Python
      •1•10•7•0•Updated Mar 19, 2026Mar 19, 2026

    • antsRegistration_affine_SyN

      Public
      Shell
      •0•2•2•0•Updated Mar 13, 2026Mar 13, 2026

    • CPCA

      Public
      Complementary principal component analysis (CPCA) for fMRI confound correction.
      Python
      •0•0•0•0•Updated Mar 5, 2026Mar 5, 2026

    • qbatch

      Public
      Python
      •
      The Unlicense
      •13•34•27•1•Updated Mar 5, 2026Mar 5, 2026

    • MAGeTBrain-nextflow

      Public
      Shell
      •
      Other
      •1•1•14•0•Updated Mar 4, 2026Mar 4, 2026

    • synthstrip_N3

      Public
      A preprocessing tool for human T1w MRIs
      Shell
      •1•2•9•2•Updated Feb 13, 2026Feb 13, 2026

    • WMH_patho_UKB

      Public
      R
      •0•1•0•1•Updated Feb 12, 2026Feb 12, 2026

    • make_slice_images

      Public
      Perl
      •0•2•4•0•Updated Feb 11, 2026Feb 11, 2026

    • preclinical_N3

      Public
      Shell
      •0•1•4•1•Updated Feb 11, 2026Feb 11, 2026

    • simpleitk_timeseries_motion_correction

      Public
      Python
      •2•1•8•1•Updated Feb 5, 2026Feb 5, 2026

    • minc-toolkit-extras

      Public
      Extra miscellaneous scripts for minc-toolkit
      Shell
      •
      Other
      •7•8•8•1•Updated Jan 30, 2026Jan 30, 2026

    • documentation

      Public
      Documentation for every thing, everything documented
      7•43•2•0•Updated Jan 15, 2026Jan 15, 2026

    • cobralib

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

    • WMH_UKB_menopause

      Public
      WMH_UKB_menopause
      R
      •0•1•0•0•Updated Sep 2, 2025Sep 2, 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

    • 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

    • RABIES_tutorial

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •3•3•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
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