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multi-atlas-segmentation

Multi Atlas Segmentation and Morphometric analysis toolkit (MASMAT) for mouse brain MRI

multi-contrast-mri-image-registration

EE 4951W Team Project

multib1_fit_z-cw_2pool

Quantification of CEST effects by simultaneous fit of Z-spectra acquired at multiple B1

multiband-rf

Code to design Multiband RF pulses

multiband-rf-pulse-design

A framework for designing RF pulse with multiband magnitude profile, arbitrary phase profile and generalized flip angle, using convex optimization. Spectral sparsity was exploited to further optimize pulse performance, such as minimizing pulse duration, transition width and total energy with flexible trade-off.

multimodalsupervoxel

The algorithm used in this code is the modification of the method Simple Linear Iterative Clustering (SLIC). Our method is optimized for medical images such as MRI, CT, etc. The contributions of our codes compared to conventional 2D and 3D superpixel are as follows: 1. Multi-modal input (works for single-modal, as well), 2. Taking the spatial resolution of the medical images into account, i.e. the voxel resolution in X and Y directions and the slice thickness.

multislicealignedsense

Tools for aligned reconstruction of multi-shot multi-slice MR.

mutlimodal-imge-registration

Multimodal image image registration main functions such as mutual information (MI), histogram segmentation, rigid transformation, and RMSE

nf-core-mrimorph

UNDER CONSTRUCTION: Mouse brain morphometry analysis pipeline for MRI imaging data

nifti-studio

A toolbox for NIfTI and Analyze medical image visualization, editing, and 3D rendering

nifti_matlab

Matlab for NIFTI support

niftyreg

This project contains command line tools to perform rigid, affine and non-linear registration of nifti or analyse images as well as utilities

nordic_raw

Matlab code for performing image reconstruction in MRI and performing the NORDIC denoising

optimized_antsmultivariatetemplateconstruction

A re-implementation of antsMultivariateTemplateConstruction2.sh using optimized image pyramid scale-space and qbatch support

peakfit

A peak-fitting tool based on MATLAB for spectroscopic data analysis.

piracy

plof

This toolbox contains demo for polynomial and Lorentzian line-shape fitting (PLOF)

pulseq

Open source framework for pulse sequences

pulseq-cest

pydpiper

Python code for flexible pipeline control

pyminc

A python interface to the MINC 2 library, allowing use of numpy arrays to access MINC data, and other such similar goodies, developed by Jason Lerch

qmrlab

Quantitative Magnetic Resonance Imaging Made Easy with qMRLab: a Software for Data Simulation, Analysis and Visualization

qmt-optimization

Quantitative Magnetization Transfer MRI Optimization Toolbox

rabies

fMRI preprocessing pipeline and analysis tools adapted for rodent images. Visit the full documentation at https://rabies.readthedocs.io/en/stable/

rat_rsfmri_preprocessing

Preprocessing toolbox for rat rs-fMRI data

reorient

A tool for reorienting and cropping MRI data

riciannet

MRI denoising used RicianNet

rminc

Statistics for MINC volumes: A library to integrate voxel-based statistics for MINC volumes into the R environment. Supports getting and writing of MINC volumes, running voxel-wise linear models, correlations, etc.; correcting for multiple comparisons using the False Discovery Rate, and more. With contributions from Jason Lerch, Chris Hammill, Jim Nikelski and Matthijs van Eede. Some additional information can be found here:

rodentmriskullstripping

U-Net based automatic Rat brain-mask Segmentation tool, developed by Hsu

sammba-mri

small mammals brain MRI