hdary

llama-agentic-system

Agentic components of the Llama Stack APIs

SlicerJupyter

Extension for 3D Slicer that allows the application to be used from Jupyter notebook

SlicerNotebooks

Examples that illustrate how to use 3D Slicer via Jupyter notebooks in Python

siemens_to_ismrmrd

Siemens ISMRMRD converter

clinica

Software platform for clinical neuroimaging studies

ipydatagrid

Fast Datagrid widget for the Jupyter Notebook and JupyterLab

uptime

Uptime for various poldracklab sites.

MRIcroGL

v1.2 GLSL volume rendering. Able to view NIfTI, DICOM, MGH, MHD, NRRD, AFNI format images.

Brain_bundle_simulator

spinalcordtoolbox

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

freesurfer

Neuroimaging analysis and visualization suite

CLaiMS

MS-lesion-segmentation

TractSeg

Automatic White Matter Bundle Segmentation

Slicer-LesionSimulatorExtension

3D Slicer extension that provides a toolkit for Multiple Sclerosis lesion simulation in multimodal MRI images, such as T1, T2, T2-FLAIR and DTI scalar maps.

LesionSeg

Multiple Sclerosis Lesion Segmentation with Tiramisu and 2.5D Stacked Slices

7T-dMRI

dMRIharmonization

Multi-site dMRI harmonization

PyDesigner

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 tutorial on PyDesigner and its usage is now available at https://www.youtube.com/watch?v=mChQFuQqX3k

7TAMI_MM

pyCirclize

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

retroMoCoBox

Retrospective motion-correction of 3D MRI k-space data in Matlab

DeepPrep

DeepPrep: An accelerated, scalable, and robust pipeline for neuroimaging preprocessing empowered by deep learning

roistats

Collecting and plotting regions-of-interest in neuroimaging data.

gradunwarp

Gradient Unwarping in Python

pyxnat

XNAT in Python

gradcorrect

BIDS app for correcting gradient non-linearities, saves corrected images as mirrored BIDS dataset, along with warp and intensity-correction fields

7TAMIBrain

template_AMU7T

Data repository containing the AMU7T atlas and template

nicMSlesions

Easy multiple sclerosis white matter lesion segmentation using convolutional deep neural networks.