DCAN-Labs/dcan-nn-unet

Stars
2
Language
Python
License
BSD 3-Clause "New...
Created over 3 years ago
Updated about 1 month ago

DCAN-Labs/dcan-nn-unet

DCAN-Labs

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Utility programs created for using nn-UNet on ABCD data.

abcd-hcp-pipeline

bids application for processing functional MRI data, robust to scanner, acquisition and age variability.

nda-abcd-s3-downloader

Tool for downloading ABCD_BIDS inputs and derivatives from the ABCD-BIDS NDA Collection 3165.

functional-random-forest

Functional Analysis with Random Forests

abcd-dicom2bids

For selectively downloading ABCD data QC'ed as good by the DAIC, converting it to BIDS standard input data, selecting the best pair of spin echo field maps, and correcting the sidecar JSON files to meet BIDS Validator spec.

compare_matrices_to_assign_networks

cifti-connectivity

Script to generate correlation matrices from BOLD dense or parcellated time series data.

infant-abcd-bids-pipeline

Human infant pipeline, based on abcd-hcp-pipeline, to process fMRI data.

file-mapper

An easy tool to copy/move/symlink files from one directory to the other!

dcan-infant-pipeline

The actual pipeline code, based on hcp, for human infants

DCAN-HCP

The DCAN Lab's version of the minimal preprocessing pipeline for the Human Connectome Project

dcan_bold_processing

functional connectivity preprocessing for resting state fMRI outputs of the dcan-fmri-pipelines

RFRF

Functional Random Forest R package

movement_regressors_power_plots

Correction of respiratory artifacts in MRI head motion estimates

BIBSnet

This BIDS App provides the utility of creating a nnU-Net anatomical MRI segmentation and mask with a infant brain trained model. It can easily be included in other processing pipelines and for circumventing JLF within Nibabies.

MarginalModelCIFTI

cdni-brain

readthedocs for CDNI collaborators and members

abcd-bids-tfmri-pipeline

Pipeline to complete within-run and between-runs analyses of task-based fMRI dense timeseries data. This tool works with data that were minimally processed using the DCAN Labs' ABCD-HCP-Pipeline, including their Collection 3165 release through NDA.

dcan-macaque-pipeline

The actual pipeline code, based on hcp, for non-human-primates - sp macaques.

ExecutiveSummary

quality control images / html viewer for the dcan-fmri-pipelines

HBCD-MADE

HBCD branch of the MADE pipeline for EEG preprocessing

brain-roi-hausdorff-distance

Computes the maximum Hausdorff distance between pairs of ROIs in a given collection of 3D ROIs.

SwipesForScienceToolkit

Tool kit for exploratory data analysis and usage of SwipesForScience JSON data, complete with anonymous sample data.

Jupyter Notebook

nhp-abcd-bids-pipeline

Non-human primate (i.e., macaque) pipeline, based on abcd-hcp-pipeline, to process fMRI data.

nda-bids-upload

For uploading BIDS data to the NDA.

heudiconv-helper

abcd-hcp-pipeline_audit

CABINET

CABINET is a utility that standardizes subsequent container execution. Emphasizing reproducibility, users can share JSONs to exactly replicate how containerized processes follow each other.

BWAS

Code to run Brain Wide Association Studies to derive PolyNeuro Risk Scores

DCAN-Labs-Website

This repository contains the code for DCAN's website

SLURM_wrappers

MachineLearning_SVM

connectotyping

ABCD_FD_analysis

This project houses the code repository for examining the factors that drive framewise displacement in the ABCD study

QSIPREP_HBCD_QC

Tool to make QC images for HBCD's QSIPREP Output

biceps_cmdln

internal-tools

Tools written by DCAN Labs and used, in common, by the DCAN pipelines.

simnibs_cifti_tools_RTD2

external-software

Tools needed for the DCAN Labs pipelines that we didn't write.

automated-subset-analysis

Automated split-half subset reliability analysis scripts written for the ABCD resource paper.