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@pnlbwh Psychiatry Neuroimaging Lab @ BWH/HMS

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    52 repositories

    • luigi-pnlpipe

      Public
      NIFTI pipeline glued together using Luigi
      Python
      •
      Other
      •7•7•13•1•Updated Jan 16, 2025Jan 16, 2025

    • pnlNipype

      Public
      PNL pipeline for NIFTI images
      Python
      •
      Other
      •15•10•19•0•Updated Jan 14, 2025Jan 14, 2025

    • tract_querier

      Public
      Implementation of the White Matter Query Language and associated tools for dMRI white matter tract extraction and analysis
      Python
      •
      Other
      •26•0•0•0•Updated Jan 10, 2025Jan 10, 2025

    • dMRIharmonization

      Public
      Multi-site dMRI harmonization
      Python
      •
      Other
      •14•46•12•0•Updated Jan 9, 2025Jan 9, 2025

    • CNN-Diffusion-MRIBrain-Segmentation

      Public
      CNN based brain masking
      Python
      •
      Other
      •10•15•2•0•Updated Jan 6, 2025Jan 6, 2025

    • HD-BET

      Public
      MRI brain extraction tool
      Python
      •
      Apache License 2.0
      •67•0•0•0•Updated Jan 6, 2025Jan 6, 2025

    • multi-shell-dMRIharmonization

      Public
      Harmonization of multi-shell diffusion MRI, an enhancement of https://github.com/pnlbwh/dMRIharmonization
      Python
      •
      Other
      •5•9•5•0•Updated Nov 19, 2024Nov 19, 2024

    • HCPpipelines

      Public
      Processing pipelines for the HCP
      Shell
      •
      Other
      •273•1•4•2•Updated Sep 17, 2024Sep 17, 2024

    • TBSS

      Public
      Tract based spatial statistics using ANTs and FSL
      Python
      •
      Other
      •7•12•9•1•Updated Jul 30, 2024Jul 30, 2024

    • diskusage-logging

      Public
      Log disk usage automatically
      Python
      •1•2•2•0•Updated Jul 29, 2024Jul 29, 2024

    • ukftractography

      Public
      3d-slicer-extension
      C
      •
      Other
      •27•26•15•3•Updated Jun 21, 2024Jun 21, 2024

    • SlicerDiffusionQC

      Public
      Quality checking of DWMRI
      3d-slicer-extension
      Python
      •
      Other
      •5•6•9•1•Updated May 16, 2024May 16, 2024

    • pnlpipe

      Public
      A Python-based framework for processing anatomical (T1, T2) and diffusion weighted images
      Python
      •
      Other
      •9•12•7•1•Updated Apr 2, 2024Apr 2, 2024

    • freesurfer-analysis

      Public
      Interactive analysis of FreeSurfer statistics using https://plotly.com/dash/
      Python
      •1•1•4•1•Updated Mar 28, 2024Mar 28, 2024

    • nifti-snapshot

      Public
      Takes snapshot of Nifti images
      Python
      •1•5•0•0•Updated Feb 18, 2024Feb 18, 2024

    • eddy-squeeze

      Public
      Visualize extra information from FSL 6.0.1 eddy outputs
      HTML
      •
      Other
      •0•4•2•0•Updated Aug 30, 2023Aug 30, 2023

    • conversion

      Public
      Various mri conversion/modification scripts
      Python
      •
      Other
      •6•21•6•0•Updated May 23, 2023May 23, 2023

    • dashboard

      Public
      A lightweight dashboard for monitoring project progress
      Python
      •0•0•0•0•Updated Jan 1, 2023Jan 1, 2023

    • pnlpipe_software

      Public
      Submodule for pnlpipe and pnlNipype software installation
      Python
      •0•0•2•0•Updated Jan 1, 2023Jan 1, 2023

    • structuralQC

      Public
      Machine learning tool for checking goodness of an anatomical scan (T1/T2)
      Jupyter Notebook
      •
      Other
      •1•1•1•0•Updated Jan 17, 2022Jan 17, 2022

    • pnl_randomise

      Public
      FSL randomise related scripts
      Python
      •4•9•4•0•Updated Jan 10, 2022Jan 10, 2022

    • pnlpipe-containers

      Public
      Containers for pnlpipe software
      Shell
      •
      Other
      •2•0•5•0•Updated Aug 23, 2021Aug 23, 2021

    • MK-Curve-PNL-Documentation

      Public
      MK-Curve PNL documentation
      0•0•0•0•Updated Mar 10, 2021Mar 10, 2021

    • tbss_containers

      Public
      Docker and Singularity containers for pnlbwh/TBSS
      Shell
      •17•0•0•0•Updated May 24, 2020May 24, 2020

    • BRAINSTools

      Public
      A suite of tools for medical image processing focused on brain analysis
      C++
      •
      Apache License 2.0
      •97•0•0•0•Updated Feb 6, 2020Feb 6, 2020

    • fsl-containers

      Public
      Experimental fsl containers for learning purpose, consult fsl license at https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
      3•5•1•0•Updated Oct 4, 2019Oct 4, 2019

    • cmd

      Public
      Submodule for pnlpipe and pnlNipype software installation
      Python
      •0•0•0•0•Updated Sep 7, 2019Sep 7, 2019

    • trainingDataT2Masks

      Public
      Shell
      •0•0•0•0•Updated Jul 2, 2019Jul 2, 2019

    • trainingDataT1AHCC

      Public
      Shell
      •1•0•0•0•Updated Jul 2, 2019Jul 2, 2019

    • mri2mrs

      Public
      Combining diffusion MRI and MRS
      MATLAB
      •
      Other
      •1•1•2•0•Updated Apr 30, 2019Apr 30, 2019