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aedes

AEDES is a graphic user interface (GUI) based tool for region of interest (ROI) analysis of (mainly) MRI images

aidamri

Atlas-based processing pipeline for structural and functional MRI mouse data

along-tract-stats

A MATLAB toolbox for performing along-tract analysis of diffusion tensor imaging (DTI) MRI tractography data.

asl-mricloud

ASL-MRICloud is hosted on braingps.mricloud.org to facilitate automated online processing of ASL MRI data.

awake-fmri-3d-models

These models are for awake fMRI (mouse)

awesome-cheatsheets

👩‍💻👨‍💻 Awesome cheatsheets for popular programming languages, frameworks and development tools. They include everything you should know in one single file.

bruker

matlab files for reading and processing Bruker MRI data

chart_demo

diffusion-tensor-images-of-rat-brain-processing

Skull-stripping and bias correction in DTI images of rat brains

errm

Code for the Extended Reference Region Model for DCE-MRI (NBM 3924)

fmri_analysis

Dump of all codes for fMRI analysis using SPM, roi analysis using Marsbar, Grey matter 3D ASL, Eprime data analysis

funconpy

Resting State fMRI Functional Connectivity Pipeline

functional-connectivity-analysis

Brain Connectivity Analysis on FMRi data in a memory task performed at Baycrest Hospital

hmri_mouse

Copy of hMRI Toolbox from (https://github.molgen.mpg.de/hMRI-group/Toolbox/wiki) adapted for mouse analysis

hyperpolarized-mri-toolbox

The goal of this toolbox is to provide research-level and prototyping software tools for hyperpolarized MRI experiments. It is currently based on MATLAB code, and includes code for designing radiofrequency (RF) pulses, readout gradients, and data reconstruction.

longitudinal-monitoring-of-aging-mouse-brain

magetbrain

Multiple Automatically Generated Templates brain segmentation algorithm

mouse-brain-atlas

Mouse Brain MRI Atlas (MBMA): both in-vivo and ex-vivo

mouse-brain-atlases_generator

Generate a package-manager-friendly mouse brain atlases collection.

mousemorph

Tools for MRI mouse brain morphometry

mousemriprep

Scripts to preprocess mouse MRI/fMRI/dMRI

nf-core-mrimorph

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

nf-core-mrimorph-1

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

preclinical-fmri-registrations

A pipeline to register denoised preclinical fMRI scans to template space

pulseqt1t2mapping

Contains pulseq definitions for T1 (VFA GRE), T2 (MESE) mapping sequences.

rodent_rsnetworks

A pipeline for rodent functional MRI analysis

rs-fmri

pre-processing for rs fMRI data aquired using pCASL sequence

rsfmri

My research project about functional brain connectivity analysis based on time-series data analysis and statistical modeling

rsfmri-preprocessing

Preprocessing pipeline for resting state MRI data

samri

Small Animal Magnetic Resonance Imaging via Python.