Review the challenges and potential of ARM-based Apple Silicon macOS for brain imaging research

Docker - Beginners | Intermediate | Advanced

Container for Freesurfer recon-all, thalamus, brainstem, hippocampus/amygdala

RNN and general weights, gradients, & activations visualization in Keras & TensorFlow

Psych 4025 Fall 2023 Semester

Preprocessing of diffusion MRI

PyTorch implementation of FastSurferCNN

Updated xnat downloader using pyxnat

Univariate and mass-univariate linear mixed-effects analysis for FreeSurfer imaging data.

A hands-free DTI, DKI, FBI and FBWM preprocessing pipeline. Information on algorithms and preprocessing steps are available at https://www.biorxiv.org/content/10.1101/2021.10.20.465189v1 A video tu…

Open-source eddy-current and head-motion correction for dMRI.

Repository for the book Simplifying Machine Learning with PyCaret.

Adaptive boosting for ordinal target variables using neural networks

Harmonization of multi-site imaging data with ComBat

MRtrix3 provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and appar…

Code used in the Meisler and Gabrieli 2022 eLife paper on fixel based analyses of reading abilities.

Automatic White Matter Bundle Segmentation

A game theoretic approach to explain the output of any machine learning model.

A game theoretic approach to explain the output of any machine learning model.

🧠💬 Articles I wrote about machine learning, archived from MachineCurve.com.

Sample parallel R scripts

DIPY is the paragon 3D/4D+ medical imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medi…

Diffusion parameter EStImation with Gibbs and NoisE Removal pipeline

Script-framework using FSL, Freesurfer and AFNI functionality for automatization and high-throughput processing of MRI data in clustered environments.

Machine learning project for implementing the RISE method for identifying key features in the input

Toolbox for the analysis of cerebellar imaging data

Code for ANTS book (Cohen, 2012, MIT Press)