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    200 repositories

    • transdiagnostic_executive_function

      Public
      Data resource that combines longitudinal multi-modal imaging data with rich clinical and cognitive phenotyping
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • hbcd_pipeline_replication_guide

      Public
      Code and instructions necessary for replicating the figures/statistics for "Diffusion MRI Processing in HBCD: Innovations and Applications"
      Python
      •0•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • xcp_d

      Public
      Post-processing of fMRIPrep, NiBabies, and HCP outputs
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •33•102•47•11•Updated Nov 3, 2025Nov 3, 2025

    • bdt

      Public
      BIDS Derivatives Transformer
      Python
      •
      Apache License 2.0
      •0•0•2•1•Updated Nov 1, 2025Nov 1, 2025

    • sypres-docs

      Public
      HTML
      •
      MIT License
      •0•0•2•5•Updated Oct 31, 2025Oct 31, 2025

    • aslprep

      Public
      Preprocessing of arterial spin labeling (ASL) data
      aslcbfbids-apps
      Python
      •
      Other
      •18•51•39•7•Updated Oct 31, 2025Oct 31, 2025

    • qsirecon

      Public
      Reconstruction of preprocessed q-space images (dMRI)
      mribidsdwidiffusion-mribids-formatdmribidsappbids-apps
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •12•14•70•12•Updated Oct 31, 2025Oct 31, 2025

    • babs

      Public
      BIDS App Bootstrap (BABS)
      Python
      •
      MIT License
      •7•10•33•7•Updated Oct 31, 2025Oct 31, 2025

    • CuBIDS

      Public
      Curation of BIDS (CuBIDS): A sanity-preserving software package for processing BIDS datasets.
      neuroscienceneuroimagingneuroinformaticspython-packagedata-curationneuroscience-methodsneuroimaging-data-sciencedata-organization
      Python
      •
      MIT License
      •13•28•47•9•Updated Oct 30, 2025Oct 30, 2025

    • qsiprep

      Public
      Preprocessing of diffusion MRI
      pipelinesdistortion-correctionbidsmotion-correctiondiffusion-mridenoising-images
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •60•167•143•8•Updated Oct 28, 2025Oct 28, 2025

    • nibs

      Public
      Myelin mapping test-retest study
      Python
      •
      MIT License
      •0•1•3•1•Updated Oct 27, 2025Oct 27, 2025

    • grmpy_opendata

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 22, 2025Oct 22, 2025

    • ModelArray

      Public
      ModelArray: an R package for statistical analysis of fixel-wise data and beyond
      rbig-datastatistical-analysisneuroimaging
      R
      •
      Other
      •3•6•18•2•Updated Oct 14, 2025Oct 14, 2025

    • aslprep_build

      Public
      Builds a base docker image for xcp-d
      Dockerfile
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•3•0•Updated Oct 13, 2025Oct 13, 2025

    • thalamocortical_development

      Public
      https://pennlinc.github.io/thalamocortical_development/
      R
      •2•4•0•0•Updated Oct 13, 2025Oct 13, 2025

    • AI2D

      Public
      Website showcasing AI2D datasets
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 10, 2025Oct 10, 2025

    • ModelArrayIO

      Public
      Companion converter software for ModelArray for converting data back and forth from the HDF5 file format.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•4•0•Updated Oct 9, 2025Oct 9, 2025

    • simbids

      Public
      Simulate BIDS MRI data and BIDS Derivatives for CI testing
      Python
      •
      Apache License 2.0
      •0•0•0•5•Updated Oct 1, 2025Oct 1, 2025

    • PennLINC.github.io

      Public
      Documentation for PennLINC
      HTML
      •
      MIT License
      •17•4•30•4•Updated Sep 22, 2025Sep 22, 2025

    • ConFixel

      Public
      Companion converter software for ModelArray for converting data back and forth from the HDF5 file format.
      pythonneuroimaging
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•7•0•Updated Sep 18, 2025Sep 18, 2025

    • qsirecon-bad

      Public
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•2•Updated Sep 8, 2025Sep 8, 2025

    • xcpd_build

      Public
      Builds a base docker image for xcp-d
      Dockerfile
      •2•2•4•0•Updated Aug 18, 2025Aug 18, 2025

    • PREPAIR

      Public
      PREPAIR is an unsupervised physiological noise correction method using magnitude and phase data instead of external recordings to identify physiological fluctuations in the brain..
      MATLAB
      •
      MIT License
      •3•0•0•0•Updated Jul 17, 2025Jul 17, 2025

    • sepia

      Public
      Matlab GUI pipeline application for quantitative susceptibility mapping (QSM)
      MATLAB
      •
      MIT License
      •16•1•0•0•Updated Jul 7, 2025Jul 7, 2025

    • clinical_dmri_benchmark

      Public
      Can we reliably get nice bundles from clinical quality dmri?
      Jupyter Notebook
      •
      MIT License
      •1•2•1•0•Updated Jul 7, 2025Jul 7, 2025

    • freesurfer-post

      Public
      Turns freesurfer directories into tabular and cifti data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jun 26, 2025Jun 26, 2025

    • lincflows

      Public
      A repository collecting workflows and interfaces used across PennLINC packages. Modeled on the nipreps repository niworkflows.
      BSD 3-Clause "New" or "Revised" License
      •0•0•1•0•Updated Jun 20, 2025Jun 20, 2025

    • ihmt_proc

      Public
      Python
      •
      Other
      •2•0•0•0•Updated Jun 6, 2025Jun 6, 2025

    • pymp2rage

      Public
      Lightweight Python package to process MP2RAGE and ME-MP2RAGE-data
      Jupyter Notebook
      •
      Other
      •16•0•0•0•Updated Jun 4, 2025Jun 4, 2025

    • luo_wm_dev

      Public
      HTML
      •0•1•0•0•Updated May 28, 2025May 28, 2025