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@CoBrALab Computational Brain Anatomy Laboratory

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    43 repositories

    • MAGeTBrain-nextflow

      Public
      Nextflow
      •
      Other
      •0•0•10•0•Updated May 29, 2025May 29, 2025

    • make_slice_images

      Public
      Shell
      •0•1•4•0•Updated May 26, 2025May 26, 2025

    • RABIES

      Public
      fMRI preprocessing pipeline and analysis tools adapted for rodent images. Visit the full documentation at https://rabies.readthedocs.io/
      Python
      •
      Other
      •18•41•63•5•Updated May 21, 2025May 21, 2025

    • twolevel_ants_dbm

      Public
      A twolevel deformation based morphometry pipeline using ants
      Python
      •
      Other
      •8•11•19•1•Updated May 16, 2025May 16, 2025

    • ODC-Mouse-Forms

      Public
      A repo containing OpenDataCapture forms for tracking mouse data gathered from experiments within the CoBra Lab
      TypeScript
      •1•1•7•0•Updated May 15, 2025May 15, 2025

    • mousefmri_acq_publication

      Public
      Contains all the code for reproducing analyses and figures in the mouse fmri acquisition guidelines paper
      Jupyter Notebook
      •0•0•0•0•Updated May 10, 2025May 10, 2025

    • optimized_antsMultivariateTemplateConstruction

      Public
      A re-implementation of antsMultivariateTemplateConstruction2.sh using optimized image pyramid scale-space and qbatch support
      Shell
      •
      Other
      •9•27•34•0•Updated Apr 29, 2025Apr 29, 2025

    • minc-toolkit-extras

      Public
      Extra miscellaneous scripts for minc-toolkit
      Shell
      •
      Other
      •7•6•8•1•Updated Apr 4, 2025Apr 4, 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
      •25•49•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
      •2•2•0•0•Updated Mar 12, 2024Mar 12, 2024

    • iterativeN3

      Public
      Shell
      •
      Other
      •0•0•10•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

    • qbatch

      Public
      Python
      •
      The Unlicense
      •13•32•28•3•Updated Mar 25, 2023Mar 25, 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•3•0•0•Updated Nov 21, 2022Nov 21, 2022

    • atlases

      Public
      Segmentations of Neuroanatomy on Hi-Res T1 and T2 MRIs and publicly available population averages in MNI space
      Python
      •
      Other
      •21•33•3•0•Updated Nov 18, 2022Nov 18, 2022

    • PyQC

      Public
      Python+Qt5 Interface for quickly quality-controlling arbitrary sets of images
      Python
      •
      GNU General Public License v3.0
      •1•1•6•0•Updated Oct 19, 2022Oct 19, 2022

    • MTR_processing

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Aug 2, 2022Aug 2, 2022

    • documentation

      Public
      Documentation for every thing, everything documented
      6•41•2•0•Updated Mar 8, 2022Mar 8, 2022

    • TractREC

      Public
      Collection of tools to perform diffusion processing and tractography.
      Python
      •
      MIT License
      •2•0•1•1•Updated Feb 26, 2022Feb 26, 2022