AFNI-based brain warping based on D99 Macaque Atlas warp scripts
Classification of par/rec MR data from Philips
Extract metadata from raw DICOM data from Siemens, Philips, or GE.
SciTran DICOM Conversion Tool
DICOM/PAR-REC conversion to nifti using Rorden's dcm2nii (v.4AUG14)
Applies the retinotopy templates from Benson et al. (2014) PLOS Comput Biol to a FreeSurfer subject output.
Estimates a first-level model for the tasks used in the ENGAGE and RAD studies.
Calculate the RMSE between a tensor fit from dtiInit and the diffusion weighted imaging data
Reorient NIfTI data and metadata fields into RAS space
Performs all, or any part of, the FreeSurfer cortical reconstruction process.
DICOM/PAR-REC conversion to nifti using Rorden's dcm2niix
Time Series Diff Analysis - Analyzes differences in slices over time to find quality issues
Does slice time correction, normalization, and smoothing on a functional image to prepare for connectivity analysis
uses SPM to realign and unwarp a functional image
use linear registration to find a mapping from functional images to structural images. also extracts brain from functionals
smooths images using SPM12
uses regression to find and remove global signal of functional data
SPM8 with MATLAB MCR 2010a
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.
Run QA metrics (displacement, signal spikes) to create a quality assurance report (png) for an fMRI NIfTI using CNI/NIMS code from @rfdougherty.
Vistasoft (mrDiffusion) preprocessing pipeline for diffusion MR data
Matlab Compiler Runtime for v9.0.1 (R2016a)
register structural images to standard templates
Automated Fiber Quantification
dtiPrep quality assurance algorithm