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cni-dcm-convert

SciTran CNI DICOM Conversion Tool

cni-dicom-mr-classifier

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

cni-qa-report-fmri

Run QA metrics (displacement, signal spikes) to create a quality assurance report (png) for an fMRI NIfTI using CNI/NIMS code

datasciencecourse

This holds iPython notebooks and lecture slides for the Intro to Data Science Master's course I teach at NYU.

dcmstack

DICOM to Nifti conversion with meta data preservation

dl_tutorial

dtiinit

Vistasoft (mrDiffusion) preprocessing pipeline for diffusion MR data

dwi-flip-bvec

Flips bvec x, y, or z

exchange

Flywheel Gear Exchange

fsl-bet

FSL's Brain Extraction Tool (BET)

fsl-fast

FMRIB's Automated Segmentation Tool

fw-gear-dtiinit-diffusion-maps

Generate diffusion maps from dt6

gadgetron

Gadgetron - Medical Image Reconstruction Framework

gannet

Gannet analysis of edited MRS data

hcppipelines

hcppipelinessingularity

Files related to running the HCP Pipelines using Singularity

heudiconv

A flexible DICOM converter for organizing brain imaging data into structured directory layouts

heudiconv-joss-paper

Repository to prepare HeuDiConv paper

ismrmrd

ISMRM Raw Data Format

mriqc

Automated Quality Control and visual reports for Quality Assesment of structural (T1w, T2w) and functional MRI of the brain

mrtrix3preproc

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

multishell-qspace-gradients

Generate a ready-to-import gradient table for a multi-shell DWI acquisition using Emmanuel Caruyer et al., 2013 uniform schemes in a Siemens scanner.

nifti-montage

Generate montage from NIfTI

nipype

Workflows and interfaces for neuroimaging packages

parametricmultisubjectfmri

Scripts for SPM, FSL and AFNI used for investigating the validity of parametric statistics for multi-subject fMRI.

pds-spring-2014

Practical Data Science Fall 2014

pfile-mr-classifier

Classification Gear for GE Pfiles

pipelines

preprocessing_tools

Issues and tips using CBI preprocessing tools

pybids

Python tools for querying and manipulating BIDS datasets.