Repositories list

• pmacsT1wPreprocessing

  Public
  Wrapper to run T1wPreprocessing container on the LPC

  Shell

  •0•0•0•0•Updated Mar 3, 2025Mar 3, 2025

• T1wPreprocessing

  Public
  Container for pre-processing T1w data before running structural analyses

  Python

  •0•0•0•0•Updated Feb 21, 2025Feb 21, 2025

• antsnetct

  Public
  Cortical thickness with ANTsPyNet

  Python

  •

  Apache License 2.0

  •0•0•4•0•Updated Feb 20, 2025Feb 20, 2025

• pmacsANTsPyNet

  Public
  Framework for running ANTsPyNet tools on the PMACS LPC

  Python

  •0•0•0•0•Updated Feb 14, 2025Feb 14, 2025

• antsct-aging

  Public
  ANTs cortical thickness pipeline container, contains a template for older individuals

  Perl

  •

  Apache License 2.0

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

• bstat

  Public
  A simple wrapper for more informative bjobs output

  Shell

  •

  Apache License 2.0

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

• penn-pet

  Public
  Development of a basic brain PET processing pipeline for the UPenn community

  Shell

  •

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

  •3•0•0•0•Updated Nov 8, 2024Nov 8, 2024

• pmacsPreps

  Public
  *prep wrapper scripts for the PMACS cluster

  Shell

  •

  MIT License

  •1•0•0•0•Updated Nov 7, 2024Nov 7, 2024

• pmacsAntsnetct

  Public
  Wrapper for submitting antsnetct jobs on the PMACS cluster

  Shell

  •0•0•0•0•Updated Oct 7, 2024Oct 7, 2024

• QuANTs

  Public
  Quality control, quantifying regional values, and querying of ANTs output

  Python

  •0•0•5•0•Updated Oct 6, 2024Oct 6, 2024

• LongitudinalThickness

  Public
  Development of longitudinal cortical thickness pipelines

  0•0•0•0•Updated Oct 4, 2024Oct 4, 2024

• pmacsSynthSeg

  Public
  Wrapper to run synthseg on the PMACS LPC

  Python

  •0•1•0•0•Updated Sep 9, 2024Sep 9, 2024

• rmsTheEchos

  Public
  creates an rms image from echos of a t1

  Python

  •0•0•0•0•Updated Sep 4, 2024Sep 4, 2024

• SynthSeg

  Public
  Containerized implementation of SynthSeg with additional preprocessing options

  Python

  •0•2•0•0•Updated Aug 16, 2024Aug 16, 2024

• hcpASLregInTauTDP

  Public
  CBF image to T1w image automated registration code, created for likely sporadic tau and tdp manuscript

  Shell

  •0•0•0•0•Updated Aug 2, 2024Aug 2, 2024

• PhantomEddyQC

  Public
  Script to check a phantom scan for eddy distortions affecting the b=0 volumes

  Shell

  •

  Apache License 2.0

  •0•0•1•0•Updated May 10, 2024May 10, 2024

• pmacsSynb0

  Public
  Wrapper for synb0 on the pmacs cluster

  Python

  •

  MIT License

  •0•0•0•0•Updated Mar 8, 2024Mar 8, 2024

• pmacsSynBOLD

  Public
  SynBOLD distortion correction on the pmacs cluster

  Python

  •0•0•0•0•Updated Mar 8, 2024Mar 8, 2024

• fwCustomDeidentification

  Public archive
  Script to generate custom de-identification profiles for Flywheel, and example profiles

  Python

  •2•0•0•0•Updated Oct 23, 2023Oct 23, 2023

• pmacsASHSThickness

  Public
  ASHS thickness pipeline, for computing thickness on ASHS segmentation

  Shell

  •0•0•0•0•Updated Jun 1, 2023Jun 1, 2023

• pmacsBrainExtraction

  Public
  Wrappers to manage brain extraction tools

  Python

  •0•0•0•0•Updated May 25, 2023May 25, 2023

• pmacsXCP_D

  Public
  Wrapper for XCP_D on the pmacs LPC

  Shell

  •

  MIT License

  •0•0•0•0•Updated May 9, 2023May 9, 2023

• antsxnet-cortical-thickness

  Public
  Cortical thickness pipeline using ANTsXNet and ANTs

  MIT License

  •0•0•0•0•Updated Aug 2, 2022Aug 2, 2022

• pmacsASHS

  Public
  Wrapper for ASHS on the PMACS LPC

  Shell

  •0•0•0•0•Updated May 16, 2022May 16, 2022

• pmacsSSHFS

  Public
  Convenience script to mount cluster directories on a local machine

  Shell

  •0•0•0•0•Updated Apr 18, 2022Apr 18, 2022

• quants-fw

  Public
  flywheel gear for running QuANTs

  Python

  •0•0•0•0•Updated Feb 18, 2022Feb 18, 2022

• ftdc_imaging_coordinator_tools

  Public
  workshopping tools for processing images in pmacs lpc, Flywheel, FSL and Freesurfer

  0•0•0•0•Updated Jul 23, 2021Jul 23, 2021

• pmacsAmicoNoddi

  Public
  Wrapper to run the AMICO implementation of NODDI on the PMACS cluster

  Shell

  •

  MIT License

  •0•0•0•0•Updated Jun 17, 2021Jun 17, 2021

• dtProcessing

  Public
  DTI processing scripts for retrospective data, no topup support

  Perl

  •0•0•0•0•Updated Oct 9, 2019Oct 9, 2019

• sagittalT1Preproc

  Public
  Pre-processing for sagittal T1 for enhanced antsCT / antsLongCT performance

  Perl

  •0•0•0•0•Updated Dec 5, 2018Dec 5, 2018