Scientific Transparency

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

Freesurfer's recon-all (v6.0.0). Built to the Flywheel Gear specification.

Chris Rorden's dcm2niix

Brain Extraction Tool (BET2) from FMRIB Software Library (FSL) v5.0.

Development versions

afq-pipeline-sdk

3-step pipeline designed to from raw diffusion data through AFQ.

Extract header general info from PAR file.

FSLMERGE (FMRIB) concatenates image files into a single output.

MRTRIX3 preprocessing

Run QA metrics (displacement, signal spikes) to create a quality assurance report for an fMRI NIfTI

Gannet: (v2.1) analysis of edited MRS data

Split multi-shell DWI data into individual shells.

Generate a montage from a NIfTI file.

SciTran Core

Reorient NIfTI data and metadata fields into RAS space by estimating and applying a canonical xform.

Calculate RMSE between the measured signal and the ADC (or dSIG) based on tensor model.

Flywheel Gear which runs FSL’s FAST.

Flywheel Gear for executing the vistasoft/mrdiffusion dtiInit preprocessing pipeline

SciTran DICOM Conversion Tool

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

SciTran Reaper

NEUROPYTHY: Retinotopy Template Generation (Benson, et. al.)

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

SPM8 with MATLAB MCR 2010a

HDFT Subsampled Recon algorithm from Schneider Lab, University of Pittsburgh.

Matlab Compiler Runtime for v9.0.1 (R2016a)

dtiinit-demo

afq-demo

reconall-demo