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@Deep-MI Deep Medical Imaging Lab (PI Reuter)

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    20 repositories

    • FastSurfer

      Public
      PyTorch implementation of FastSurferCNN
      Jupyter Notebook
      •
      Apache License 2.0
      •137•532•14•1•Updated Aug 14, 2025Aug 14, 2025

    • BrainPrint

      Public
      A python-only derivative of the original BrainPrint scripts
      Python
      •
      MIT License
      •9•12•0•0•Updated Aug 11, 2025Aug 11, 2025

    • WhipperSnapPy

      Public
      Python OpenGL Tool for Screenshots of Surface Overlays
      Python
      •
      MIT License
      •8•1•1•1•Updated Aug 11, 2025Aug 11, 2025

    • LaPy

      Public
      Toolbox for Differential Geometry on Triangle and Tetrahedra Meshes (FEM, Laplace, Poisson, Heat Flow ...)
      Python
      •
      MIT License
      •15•89•3•0•Updated Aug 11, 2025Aug 11, 2025

    • fsqc

      Public
      A set of quality control scripts for FreeSurfer- and FastSurfer-processed structural MRI data
      Python
      •
      MIT License
      •16•63•3•0•Updated Aug 7, 2025Aug 7, 2025

    • olf-bulb-segmentation

      Public
      Automated Olfactory Bulb Segmentation Pipeline for T2-Weighted MRI
      olfactory-bulb-segmentation
      Python
      •
      Apache License 2.0
      •3•10•0•0•Updated Aug 4, 2025Aug 4, 2025

    • hipsta

      Public
      HIPSTA - a python package for hippocampal shape and thickness analysis
      Python
      •
      MIT License
      •1•5•0•1•Updated Jul 28, 2025Jul 28, 2025

    • Deep-MI.github.io

      Public
      Deep Medical Imaging Lab Webpage
      TeX
      •
      MIT License
      •16•2•0•0•Updated Jun 20, 2025Jun 20, 2025

    • YODA

      Public
      You Only Denoise once or Average (YODA) - A diffusion-based 2.5D medical image translation model with noise-supression
      Python
      •
      Apache License 2.0
      •1•3•0•0•Updated May 6, 2025May 6, 2025

    • LIT

      Public
      FastSurfer Lesion Inpainting Tool (FastSurfer-LIT) for lesion inpainting e.g. for whole brain segmentation and cortical surface reconstruction in the presence of tumor, surgical cavities or other abnormalities
      Python
      •
      Apache License 2.0
      •3•11•0•1•Updated Apr 9, 2025Apr 9, 2025

    • segmentation_labeling

      Public
      A labeling tool for comparative segmentation labeling
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025

    • fslmer

      Public
      Univariate and mass-univariate linear mixed-effects analysis for FreeSurfer imaging data.
      R
      •
      Other
      •1•8•1•0•Updated Jan 22, 2025Jan 22, 2025

    • VINNA4neonates

      Public
      Newborn Whole Brain Segmentation with VINNA
      Python
      •
      Apache License 2.0
      •0•0•1•0•Updated Jan 9, 2025Jan 9, 2025

    • head-motion-tools

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated Nov 11, 2024Nov 11, 2024

    • DISCUS

      Public
      The repository contains code for the Geometric Deep Learning for Diffusion MRI Signal Reconstruction with Continuous Samplings (DISCUS) project
      Python
      •0•5•1•0•Updated Apr 22, 2024Apr 22, 2024

    • head-motion-from-MRI

      Public
      Code for the paper "Estimating Head Motion from MRI", which predicts motion scores directly from MRI images.
      Python
      •
      Apache License 2.0
      •2•4•0•0•Updated Mar 22, 2024Mar 22, 2024

    • 3d-neuro-seg

      Public
      Repository to our 3d neuro-anatomic segmentation method submitted to the MIDL 2022 conference
      Python
      •
      Apache License 2.0
      •1•4•1•0•Updated Jul 25, 2022Jul 25, 2022

    • FatSegNet

      Public
      Deep CNN for Abdominal Adipose Tissue Segmentation on Dixon MRI
      deep-learningimage-segmentationmedical-image-processingmri-segmentationabdominal-adipose-tissuedixon-mri
      Python
      •
      Apache License 2.0
      •13•23•1•0•Updated Apr 7, 2022Apr 7, 2022

    • fastsurfer-webpage

      Public
      Jekyll Webpage for the FastSurfer project
      HTML
      •
      MIT License
      •159•1•0•0•Updated Jan 15, 2022Jan 15, 2022

    • BrainPrint-legacy

      Public
      Python scripts for shape analysis of neuroimaging data (wrapping around shapeDNA and FreeSurfer)
      Python
      •7•20•0•0•Updated Feb 3, 2021Feb 3, 2021