Daniel Jörgens's repositories
project_template
Project folder template for my projects.
neurocontainers
The containers can be used in combination with our transparent singularity or neurocommand tool, that wrap the executables inside a container to make them easily available for pipelines
bidscoin
BIDScoin converts your source-level neuroimaging data to BIDS
neurodocker
Generate custom Docker and Singularity images, and minimize existing containers
randomised_filtering
Code for randomised tractogram filtering using rSIFT
mne-bids
MNE-BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python.
mne-bids-pipeline
Automatically process entire electrophysiological datasets using MNE-Python.
nipype
Workflows and interfaces for neuroimaging packages
3D-CycleGan-Pytorch-MedImaging
Pytorch pipeline for 3D image domain translation using Cycle-Generative-Adversarial-networks, without paired examples.
pytorch-ssim-3D
pytorch structural similarity (SSIM) loss for 3D images
freesurfer_bids_app
recon-all from FreeSurfer
datalad
Keep code, data, containers under control with git and git-annex
tractoflow
TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity
deepsphere-pytorch
DeepSphere: a graph-based spherical CNN (PyTorch)
bidsconv
Command-line tool to convert multi-subject raw dicoms to a full BIDS formatted dataset
hodaie-teem
Fork of TEEM library for the Hodaie Lab
contrastive-unpaired-translation
Contrastive unpaired image-to-image translation, faster and lighter training than cyclegan (ECCV 2020, in PyTorch)
BasicSR
Open Source Image and Video Restoration Toolbox for Super-resolution, Denoise, Deblurring, etc. Currently, it includes EDSR, RCAN, SRResNet, SRGAN, ESRGAN, EDVR, etc. Also support StyleGAN2, DFDNet.
codeare
Common data exchange and reconstruction engine for MRI
moab_taskman
Task manager for handling many long running machine learning experiments
scilpy
The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox
docker-pytorch
A Docker image for PyTorch
baselines
OpenAI Baselines: high-quality implementations of reinforcement learning algorithms