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afq-pipeline

Flywheel Gear that runs the AFQ processing pipeline

ants_registrationsynquick

asl_processing

Processing scripts for ASL data to extract cerebral blood flow (CBF) and cerebrovascular reactivity (CVR) maps

code_for_paper_myo-inositol_goschel2021

code for: Göschel, L., Fillmer, A., Dell'Orco, A., Melin, J., Aydin, S., Kurz, L., Riemann, L.T., Wang, H., Ittermann, B., Rujescu, D., Pendrill, L., Köbe, T. and Flöel, A. (2022), Associations between the glial marker myo-inositol measured by 7T MRS and other AD-relevant measures. Alzheimer's Dement., 18: e069340. https://doi.org/10.1002/alz.06934

dcm2niix

Flywheel Gear for the execution of dcm2niix

faceoff

ANTs-based commandline utilities for (1) consistent, super-fast defacing of anatomical MRI images (2) dielectric pad masking

freesurfer-recon-all

Performs all, or any part of, the FreeSurfer cortical reconstruction process.

ivim-toolbox

This toolbox is dedicated to model fitting and simulation for Intra-Voxel Incoherent Motion (IVIM) MR imaging. It gathers scripts, on the one hand, to fit IVIM bi-exponential signal representation voxel-wise and, on the other hand, to run Monte Carlo simulations in order to assess the estimation error on parameters as well as the minimum required SNR to get accurate estimation.

ivim_analysis

ivim_fitting

Intra voxel incoherent motion fitting

layerdmri

matlab-mcr

Matlab Compiler Runtime

mp2rage-related-scripts

MP2RAGE Scripts - T1 map correction & Background noise removal

myelin_map

pattern_regression

Codes for our paper on NeuroImage - comparison of pattern regression algorithms and evaluation of sample size impact.

pattern_regression_clean

Codes for pattern regression with detailed manual

pattern_regression_matlab

Matlab codes for support vector regression (SVR) and revelance vector regression (RVR) analysis with cross validation to evaluate the prediction power.

presurfer

Scripts to prepare MP2RAGE for Freesurfer

qsm

Hongfu Sun's MATLAB codes for QSM reconstruction pipeline.

qsm_oef

Data & code for the "Elevated brain oxygen extraction fraction measured by MRI susceptibility relates to perfusion status in acute ischemic stroke" study by Fan et al.

quicknat_pytorch

PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty

spinalcordtoolbox

Comprehensive and open-source library of analysis tools for MRI of the spinal cord.

spm8-mcr-v713

SPM8 with MATLAB MCR 2010a

whole_brain_project