Repositories list

• sypres-docs

  Public
  HTML

  •

  MIT License

  •0•0•1•3•Updated May 2, 2025May 2, 2025

• simbids

  Public
  Simulate BIDS MRI data and BIDS Derivatives for CI testing

  Python

  •

  Apache License 2.0

  •0•0•0•1•Updated May 1, 2025May 1, 2025

• babs

  Public
  BIDS App Bootstrap (BABS)

  Python

  •

  MIT License

  •8•8•26•1•Updated Apr 29, 2025Apr 29, 2025

• qsiprep

  Public
  Preprocessing of diffusion MRI

  pipelinesdistortion-correctionbids+ 3motion-correctiondiffusion-mridenoising-images

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •58•153•115•8•Updated Apr 28, 2025Apr 28, 2025

• xcp_d

  Public
  Post-processing of fMRIPrep, NiBabies, and HCP outputs

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •28•91•42•13•Updated Apr 28, 2025Apr 28, 2025

• clinical_dmri_benchmark

  Public
  Can we reliably get nice bundles from clinical quality dmri?

  Jupyter Notebook

  •

  MIT License

  •0•1•1•0•Updated Apr 28, 2025Apr 28, 2025

• aslprep

  Public
  Preprocessing of arterial spin labeling (ASL) data

  aslcbfbids-apps

  Python

  •

  Other

  •15•48•42•7•Updated Apr 28, 2025Apr 28, 2025

• PennLINC.github.io

  Public
  Documentation for PennLINC

  HTML

  •

  MIT License

  •17•4•29•3•Updated Apr 22, 2025Apr 22, 2025

• qsirecon

  Public
  Reconstruction of preprocessed q-space images (dMRI)

  mribidsdwi+ 5diffusion-mribids-formatdmribidsappbids-apps

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •10•9•66•7•Updated Apr 18, 2025Apr 18, 2025

• CuBIDS

  Public
  Curation of BIDS (CuBIDS): A sanity-preserving software package for processing BIDS datasets.

  neuroscienceneuroimagingneuroinformatics+ 5python-packagedata-curationneuroscience-methodsneuroimaging-data-sciencedata-organization

  Python

  •

  MIT License

  •12•25•44•8•Updated Apr 16, 2025Apr 16, 2025

• babs-yamls-cubic

  Public
  Shell

  •

  MIT License

  •0•0•0•0•Updated Apr 4, 2025Apr 4, 2025

• grmpy_opendata

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Apr 3, 2025Apr 3, 2025

• luo_wm_dev

  Public
  HTML

  •0•0•0•0•Updated Mar 31, 2025Mar 31, 2025

• cubic-environment-yamls

  Public
  MIT License

  •0•0•1•0•Updated Mar 27, 2025Mar 27, 2025

• pNet

  Public
  pNet is a Python package for computing personalized, sparse, non-negative large-scale functional networks from functional magnetic resonance imaging (fMRI) data, particularly resting state fMRI data.

  Python

  •1•0•0•0•Updated Mar 21, 2025Mar 21, 2025

• ModelArray

  Public
  ModelArray: an R package for statistical analysis of fixel-wise data and beyond

  rbig-datastatistical-analysis+ 1neuroimaging

  R

  •

  Other

  •3•5•17•2•Updated Mar 14, 2025Mar 14, 2025

• macedo_tracometry

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Mar 4, 2025Mar 4, 2025

• xcpd_build

  Public
  Builds a base docker image for xcp-d

  Dockerfile

  •2•2•4•0•Updated Jan 17, 2025Jan 17, 2025

• qsirecon_build

  Public
  Docker build for QSIRecon

  Dockerfile

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• thalamocortical_development

  Public
  https://pennlinc.github.io/thalamocortical_development/

  R

  •1•1•0•0•Updated Jan 8, 2025Jan 8, 2025

• smripost-linc

  Public
  Aggregate interesting derivatives from sMRIPrep/Freesurfer derivatives

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•6•1•Updated Jan 7, 2025Jan 7, 2025

• test_dashboard

  Public
  HTML

  •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

• aslprep_build

  Public
  Builds a base docker image for xcp-d

  Dockerfile

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•3•0•Updated Nov 25, 2024Nov 25, 2024

• TheWay

  Public
  Boilerplate scripts for running workflows on Penn clusters

  Shell

  •

  BSD 3-Clause "New" or "Revised" License

  •11•5•2•12•Updated Nov 25, 2024Nov 25, 2024

• .github

  Public
  0•0•0•0•Updated Nov 22, 2024Nov 22, 2024

• ingress2qsirecon

  Public
  A tool for ingressing outputs from other processing pipelines (e.g., HCP, UKB) for use in QSIRecon.

  dwimri-reconstruction

  Python

  •

  MIT License

  •1•0•0•0•Updated Nov 18, 2024Nov 18, 2024

• qsiprep_build

  Public
  Builds the dependencies for qsiprep

  Dockerfile

  •

  Apache License 2.0

  •3•2•1•1•Updated Nov 13, 2024Nov 13, 2024

• GRMPY_clinical_data

  Public
  0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

• ingress2xcpd

  Public
  A tool for ingressing outputs from other processing pipelines (e.g., HCP, UKB) for use in XCP_D.

  Python

  •

  MIT License

  •1•0•0•0•Updated Oct 23, 2024Oct 23, 2024

• open-physio-data

  Public
  Open fMRI datasets with concurrent physio data. Focused on physio measures that correlate with autonomic state.

  MIT License

  •0•0•3•0•Updated Oct 15, 2024Oct 15, 2024