Philip Cook

Cortical thickness pipelines using ANTsPyNet

CNDS e-field modeling pipeline container with FreeSurfer, FSL, AFNI, SimNIBS

FTDC preprocessing for T1w images. Includes neck trimming and brain extraction with HD-BET.

SynthSeg container, allows input of a brain mask to better center cropped FOV

Containerized SynthSeg

Micromamba container for FireANTs

Containerized ANTsPyNet

HD-BET brain extraction tool from https://github.com/MIC-DKFZ/HD-BET

Centos 7 base image for building ANTs. Includes GCC 11 and CMake 3.31.5

ANTs cortical thickness with a custom aging template

simnimbs3 and Matlab runtime

Containerized version of SimNIBS 4: https://simnibs.github.io/simnibs/build/html/index.html

Docker build of trekker https://github.com/dmritrekker/trekker

Testing SynBold-DISCO pipelines with fmriprep. More details to follow

Basic container with ANTsR

Containerized interface to compute NODDI using AMICO

Base container for AMICO

Facemasking code for HCP data

Deep learning ANTs cortical thickness pipeline

ANTsRNet containers