Alternatives and similar repositories for RodentMRISkullStripping

Users that are interested in RodentMRISkullStripping are comparing it to the libraries listed below

• GT-EmoryMINDlab / rodent-whole-brain-preprocessing-recipe

  View on GitHub
  A generally applicable whole-brain preprocessing toolbox for mice and rats
  ☆12Jul 11, 2024Updated last year
• yu02019 / BEN

  View on GitHub
  ☆31May 17, 2024Updated last year
• nipreps / nirodents

  View on GitHub
  ☆13Jul 2, 2024Updated last year
• neurolabusc / Bru2Nii

  View on GitHub
  Bruker ParaVision to NIfTI conversion
  ☆14May 11, 2020Updated 5 years ago
• BrkRaw / brkraw

  View on GitHub
  A modular toolkit for Bruker MRI raw-data handling.
  ☆50Feb 3, 2026Updated last week
• Aswendt-Lab / AIDAconnect

  View on GitHub
  Mouse brain network analysis of rs-fMRI and DTI data using graph theory
  ☆10Jan 16, 2026Updated 3 weeks ago
• VitoLin21 / Rodent-Skull-Stripping

  View on GitHub
  A General Rodent MRI Skull-Stripping Tool Based on Multi-Center Data
  ☆10Dec 7, 2024Updated last year
• Hierakonpolis / MU-Net

  View on GitHub
  Multi-task U-Net for the simultaneous segmentation and skull-stripping of mouse brain MRI
  ☆23Aug 20, 2021Updated 4 years ago
• AlanKuurstra / pyqsm

  View on GitHub
  ☆12Nov 27, 2019Updated 6 years ago
• grandjeanlab / MouseMRIPrep

  View on GitHub
  Scripts to preprocess mouse MRI/fMRI/dMRI
  ☆10May 22, 2024Updated last year
• dama-lab / mouse-brain-atlas

  View on GitHub
  Multi-Template Mouse Brain MRI Atlas (MBMA): both in-vivo and ex-vivo
  ☆27Jan 20, 2024Updated 2 years ago
• HennigJue / single-shot-spiral-TSE

  View on GitHub
  MatLab code to create single shot spiral TSE sequences to be run using the Pulseq sequence programming environment
  ☆13Sep 1, 2025Updated 5 months ago
• Aswendt-Lab / AIDAmri

  View on GitHub
  Atlas-based Imaging Data Analysis Pipeline (AIDA) for structural and functional MRI of the mouse brain
  ☆35Jan 16, 2026Updated 3 weeks ago
• grandjeanlab / MultiRat

  View on GitHub
  A Rat fMRI multi-center study
  ☆33Aug 12, 2022Updated 3 years ago
• ntustison / ANTsXMouseBrainMapping

  View on GitHub
  The ANTsX Ecosystem for Mapping the Mouse Brain
  ☆17Dec 2, 2025Updated 2 months ago
• mchiew / recon-tools-matlab

  View on GitHub
  MR Image Reconstruction Tools for MATLAB
  ☆16Aug 10, 2022Updated 3 years ago
• cantin-ortiz / molecular-atlas

  View on GitHub
  This repository contains the code used for the paper "Molecular Atlas of the Adult Mouse Brain".
  ☆16Feb 26, 2021Updated 4 years ago
• dama-lab / masmat

  View on GitHub
  Multi Atlas Segmentation and Morphometric analysis toolkit (MASMAT) for mouse brain MRI
  ☆41Nov 28, 2025Updated 2 months ago
• BRAIN-TO / GIRFReco.jl

  View on GitHub
  An Open-Source End-to-End Pipeline for Spiral Magnetic Resonance Image (MRI) Reconstruction in Julia
  ☆20Jul 24, 2025Updated 6 months ago
• jonbmartin / sigpy-rf-tutorials

  View on GitHub
  Collection of tutorial information and demonstrations for the sigpy-rf toolbox
  ☆21Jun 13, 2025Updated 8 months ago
• CoBrALab / RABIES

  View on GitHub
  fMRI preprocessing pipeline and analysis tools adapted for rodent images. Visit the full documentation at https://rabies.readthedocs.io/
  ☆50Updated this week
• cookpa / pipedream

  View on GitHub
  PipeDream - open source neuroimaging pipelines
  ☆17Aug 29, 2019Updated 6 years ago
• mchiew / grappa-tutorial

  View on GitHub
  A MATLAB-based tutorial on GRAPPA parallel imaging reconstruction for MRI
  ☆22Nov 14, 2022Updated 3 years ago
• zl376 / segDGM_CNN

  View on GitHub
  Segment Deep Gray Matter on QSM images using 3D CNN
  ☆19Sep 24, 2018Updated 7 years ago
• utcsilab / t2shuffling-support

  View on GitHub
  Demonstration code for the MRM manuscript, "T2 Shuffling: Sharp, Multi-Contrast, Volumetric Fast Spin-Echo Imaging"
  ☆20Jan 13, 2025Updated last year
• dterstege / FASTMAP

  View on GitHub
  ImageJ Plugin for Flexible Atlas Segmentation Tool for Multi-Area Processing
  ☆24Jul 4, 2022Updated 3 years ago
• QMICodeBase / TORTOISEV4

  View on GitHub
  Official TORTOISE Diffusion MRI Processing Pipeline V4 Source Code and Documentation
  ☆33Dec 19, 2025Updated last month
• Washington-University / NHPPipelines

  View on GitHub
  Enhancements of HCP Pipelines for non-human primates
  ☆30Jul 7, 2022Updated 3 years ago
• nmpowell / mousemorph

  View on GitHub
  Tools for MRI mouse brain morphometry
  ☆32Jan 16, 2017Updated 9 years ago
• isi-nmr / brukerapi-python

  View on GitHub
  A Python package providing I/O interface for Bruker data sets
  ☆29Feb 2, 2026Updated last week
• nipoppy / nipoppy

  View on GitHub
  Lightweight framework for neuroimaging-clinical data organization/processing
  ☆37Feb 6, 2026Updated last week
• hansenms / ismrm_sunrise_matlab

  View on GitHub
  Source code for the ISMRM Sunrise Recon Course
  ☆36Apr 28, 2014Updated 11 years ago
• SebastianoF / bruker2nifti

  View on GitHub
  Medical image format converter: from raw Bruker ParaVision to nifti.
  ☆31Dec 31, 2023Updated 2 years ago
• mathieuboudreau / qsm-tools

  View on GitHub
  List of open-source quantitative susceptibility mapping (QSM) MRI software packages and data
  ☆74May 19, 2023Updated 2 years ago
• DietrichBE / ismrmrd-viewer

  View on GitHub
  ISMRM Raw Data Viewer
  ☆10Feb 12, 2020Updated 6 years ago
• lamyj / dicomifier

  View on GitHub
  A medical image converter
  ☆32Jul 20, 2025Updated 6 months ago
• BioimageAnalysisCoreWEHI / napari_lattice

  View on GitHub
  Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for …
  ☆14Feb 4, 2026Updated last week
• nipreps / fmriprep-rodents

  View on GitHub
  fMRIPrep for Rodents
  ☆13Jun 6, 2023Updated 2 years ago
• b-heifets / UNRAVEL

  View on GitHub
  UNRAVEL: UN-biased high-Resolution Analysis and Validation of Ensembles using Light sheet images
  ☆13Updated this week