Repositories list

• nifti-montage

  Public
  Generate montage from NIfTI

  Python

  •1•0•0•0•Updated Jun 29, 2024Jun 29, 2024

• mrtrix3preproc

  Public
  mrtrix3preproc runs the mrTrix3 preprocessing pipeline in the diffussion data. It uses FSLs topup when the optional inverted phase encoding files are found, otherwise uses the eddy tool. It performs some other denoising steps, and it can normalize or align to acpc the data

  Shell

  •7•0•0•0•Updated Jun 29, 2024Jun 29, 2024

• fsl-fast

  Public
  FMRIB's Automated Segmentation Tool

  Shell

  •2•2•0•0•Updated Jun 29, 2024Jun 29, 2024

• fsl-bet

  Public
  FSL's Brain Extraction Tool (BET)

  Shell

  •2•1•0•0•Updated Jun 29, 2024Jun 29, 2024

• gannet

  Public
  Gannet analysis of edited MRS data

  Shell

  •3•0•2•2•Updated Mar 14, 2024Mar 14, 2024

• dtiinit

  Public
  Vistasoft (mrDiffusion) preprocessing pipeline for diffusion MR data

  Python

  •2•0•4•1•Updated Mar 14, 2024Mar 14, 2024

• afni-brain-warp

  Public
  AFNI-based brain warping based on D99 Macaque Atlas warp scripts

  Shell

  •0•0•3•1•Updated Dec 16, 2022Dec 16, 2022

• afq-pipeline-sdk

  Public
  AFQ Pipeline Gear using Flywheel SDK

  Python

  •0•0•0•0•Updated Dec 16, 2022Dec 16, 2022

• qa-dtiprep

  Public
  dtiPrep quality assurance algorithm

  Python

  •

  Apache License 2.0

  •0•1•0•0•Updated Dec 16, 2022Dec 16, 2022

• dti-error

  Public
  Calculate the RMSE between a tensor fit from dtiInit and the diffusion weighted imaging data

  MATLAB

  •

  Apache License 2.0

  •0•2•3•0•Updated Nov 23, 2021Nov 23, 2021

• afq-pipeline

  Public
  Flywheel Gear that runs the AFQ processing pipeline

  MATLAB

  •9•2•1•0•Updated Sep 29, 2021Sep 29, 2021

• dicom-mr-classifier

  Public archive
  Extract metadata from raw DICOM data from Siemens, Philips, or GE.

  Python

  •6•5•2•0•Updated Aug 2, 2021Aug 2, 2021

• dcm2niix

  Public archive
  DICOM/PAR-REC conversion to nifti using Rorden's dcm2niix

  Shell

  •4•4•0•0•Updated Dec 15, 2020Dec 15, 2020

• freesurfer-recon-all

  Public
  Performs all, or any part of, the FreeSurfer cortical reconstruction process.

  Shell

  •

  Other

  •4•1•0•1•Updated Oct 26, 2020Oct 26, 2020

• mrq

  Public
  Flywheel Gear to execute mrQ from Mezer Lab

  MATLAB

  •0•0•1•0•Updated Sep 11, 2020Sep 11, 2020

• parrec-mr-classifier

  Public
  Classification of par/rec MR data from Philips

  Python

  •0•0•0•1•Updated Apr 16, 2020Apr 16, 2020

• dcm-convert

  Public
  SciTran DICOM Conversion Tool

  Python

  •2•0•4•0•Updated Jun 23, 2019Jun 23, 2019

• PRF

  Public
  PRF analysis with the analyzePRF code

  MATLAB

  •

  MIT License

  •0•0•0•0•Updated May 21, 2019May 21, 2019

• fslmerge

  Public
  Uses fslmerge from FSL to merge datasets

  Shell

  •0•0•0•0•Updated Oct 17, 2018Oct 17, 2018

• fsl-eddy

  Public
  Run FSL's Eddy tool

  0•0•0•0•Updated Sep 21, 2018Sep 21, 2018

• dcm2nii

  Public
  DICOM/PAR-REC conversion to nifti using Rorden's dcm2nii (v.4AUG14)

  Shell

  •0•0•0•0•Updated Jun 16, 2018Jun 16, 2018

• afq-browser

  Public
  Gear to generate files for afq browser

  Python

  •0•0•0•0•Updated Jun 14, 2018Jun 14, 2018

• dwi-split-shells

  Public
  Split mutlti-shell dwi data into individual shells

  MATLAB

  •

  MIT License

  •0•0•0•0•Updated May 23, 2018May 23, 2018

• pyafq

  Public
  Python implementation of AFQ

  1•0•0•0•Updated May 14, 2018May 14, 2018

• dwi-norm-flip

  Public
  Normalize DWI data

  0•0•0•0•Updated May 7, 2018May 7, 2018

• retinotopy-templates

  Public
  Applies the retinotopy templates from Benson et al. (2014) PLOS Comput Biol to a FreeSurfer subject output.

  Shell

  •

  Other

  •0•2•4•0•Updated Jun 20, 2017Jun 20, 2017

• afni-brain-coreg

  Public
  Co-Register a functional to an anatomical.

  Python

  •0•0•0•1•Updated Apr 12, 2017Apr 12, 2017

• apply-canonical-xform

  Public
  Reorient NIfTI data and metadata fields into RAS space

  Shell

  •0•1•0•0•Updated Dec 14, 2016Dec 14, 2016

• spm8-mcr-v713

  Public
  SPM8 with MATLAB MCR 2010a

  2•1•0•0•Updated Nov 5, 2016Nov 5, 2016

• hdft-subsampled-recon

  Public
  Computes a transformation of multi-shell diffusion weighted data to a set of Spherical Harmonic coefficients and outputs 4D Spherical Harmonic coefficient data. This is a first step in the Schneider Lab HDFT diffusion reconstruction process.

  Python

  •0•0•0•0•Updated Nov 4, 2016Nov 4, 2016