djoerch

alps

Bash script to compute DTI-ALPS

GCN_SCZ_Classification

gantt-for-you-track

Gantt charts for YouTrack. Web app that builds a Gantt chart from the issues in a YouTrack saved search. Includes both the past (reconstructed from activity log) and the future (computed from issue metadata).

brainage-prediction-mri

Predicting the age of the brain with minimally processed T1-weighted MRI data

multiscalebrainparcellator

Multi-Scale Brain Parcellator, part of the Connectome Mapping Toolkit (CMTK), is a BIDS App that implements a full anatomical MRI processing pipeline, from raw T1w data to structural brain parcellation at five different scales.

KUL_FWT

Automated tractography using MRTrix3 CSD based on subject-specific parcellations from FreeSurfer and MultiScaleBrainParcellator

aodf-toolkit

Python toolkit for estimating asymmetric ODFs by filtering a symmetric ODF image

MedSAM

Segment Anything in Medical Images

FiberTractSegmentation

ACCURATE CORRESPONDING FIBER TRACT SEGMENTATION VIA FIBERGEOMAP LEARNER

radtract

RadTract: enhanced tractometry with radiomics-based imaging biomarkers for improved predictive modelling.

fsub_extractor

Software that functionally segments white matter connections to generate task-specific subcomponents of fiber bundles.

TractSegWithLabelEmbedding

deepsphere-pytorch

DeepSphere: a graph-based spherical CNN (PyTorch)

p3_deepsphere

DeepSphere: a graph-based spherical CNN (PyTorch)

3D-CycleGan-Pytorch-MedImaging

Pytorch pipeline for 3D image domain translation using Cycle-Generative-Adversarial-networks, without paired examples.

PytorchGeometricTutorial

Pytorch Geometric Tutorials

medigan

medigan - A Python Library of Pretrained Generative Models for Medical Image Synthesis

PreQual

An automated pipeline for integrated preprocessing and quality assurance of diffusion weighted MRI images

containers-scilus

Files needed to build a container to run all scilus flows.

fs-docker

Dockerfiles for FreeSurfer

probconnatlas

PCNtoolkit

Toolbox for normative modelling and spatial inference of neuroimaging data. https://pcntoolkit.readthedocs.io/en/latest/

ivy

Convert ML Code Between Frameworks

hodaie-teem

Fork of TEEM library for the Hodaie Lab

sagit

Perinatal_SR_Autoencoder

Network code for autoencoder training on dMRI pre-term newborns of the developing Human Connectome Project (dHCP)

bidscoin

BIDScoin converts your source-level neuroimaging data to BIDS

mne-connectivity

Connectivity algorithms that leverage the MNE-Python API.

mne-bids

MNE-BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python.

pybids

Python tools for querying and manipulating BIDS datasets.