aghaeifar

Python

All Algorithms implemented in Python

gitignore

A collection of useful .gitignore templates

cmake-examples

Useful CMake Examples

BayesianOptimization

A Python implementation of global optimization with gaussian processes.

zotero-night

Night theme for Zotero UI and PDF

NeuroKit

NeuroKit2: The Python Toolbox for Neurophysiological Signal Processing

ANTs

Advanced Normalization Tools (ANTs)

HighFive

HighFive - Header-only C++ HDF5 interface

qMRLab

Quantitative MRI Made Easy with qMRLab: MRI software for data Simulation, analysis and visualization

eigen-cuda

MWE for using the Eigen library in CUDA kernels

mri-simulator

MRI simulator for educational purposes written in MATLAB

imtool3D_td

3D Image Viewer with ROI tools for Matlab ( NIFTI viewer, Manual segmentation )

TinyMAT

C/C++ library to handle writing simple Matlab(r) MAT file

awesome-mri

Awesome Magnetic Resonance Imaging (MRI)

nifti_clib

C libraries for NIFTI support

shimming-toolbox

Code for performing static, dynamic and real-time shimming using external and internal MRI shim coils

mapVBVD

Matlab/octave tool to read twix raw data from Siemens MRI scanners.

GadgetronOnlineClass

NIfTIspace

A single NIfTI image saved with all 48 spatial rotation permutations

mrTools

mrTools - matlab based tools for fMRI

Sequence_Github

VB17 Sequence Protocols. A collection of pdfs of sequence protocols that where used in my publications. Mostly VASO, Multi-echo, SMS, 3D-EPI, low resolution up to sub-millimeter fMRI

pyCoilGen

Magnetic Field Coil Generator for Python, ported from CoilGen

grappa-tutorial

A MATLAB-based tutorial on GRAPPA parallel imaging reconstruction for MRI

monte-carlo-simulation-recipes

Recipes of Monte Carlo simulations in Fieremans and Lee, NeuroImage 2018

recoMRD

Python scripts to read and reconstruct ismrmrd (mrd) format

SpinWalk

SpinWalk, a framework for Monte-Carlo simulation to model spins random walk within a microvascular network. SpinWalk can be also employed to simulate diffusion in a microstructure substrates.

ismrmrd_to_nifti

siemens_to_ismrmrd

Siemens ISMRMRD converter

phase_unwrap

Multi-dimensional phase unwrapping

streamFunctionMethod