HBCD Processing Pipelines🔗
The HBCD processing pipelines are a collection of modular tools used to process HBCD Study data, including magnetic resonance imaging/spectroscopy (MRI/MRS), electroencephalography (EEG), and biosensor data. Pipeline outputs are provided within the data release as file-based derivatives. All community pipelines used for HBCD data processing must follow HBCD Processing & Derivative Data Standards. The table below includes links to the NMIND Evaluated Tools page for each pipeline.
Full technical details on how each pipeline was executed and configured is available in the HBCD Processing documentation, with pipeline-specific parameters detailed under Tool Names (e.g., 'File Selection For Processing' and 'Quality Control Selection Information').
HBCD Processing Pipelines & Relevant Links to Documentation
| Pipeline | Derivatives | Description | File Tree | NMIND |
|---|---|---|---|---|
| Structural & Functional MRI | ||||
| MRIQC | mriqc/ |
Extracts image quality metrics from raw MRI data | ||
| BME-X | bme_x/ |
Structural pipeline for T1w/T2w image quality enhancement | ||
| BIBSNet | bibsnet/ |
Deep learning model for brain segmentation | ||
| Infant-fMRIPrep | nibabies/ |
Structural and functional MRI preprocessing pipeline | ||
| FreeSurfer | freesurfer/ |
Infant FreeSurfer surface reconstruction workflow run in fMRIPrep | — | |
| M-CRIB-S | mcribs/ |
Neonatal surface reconstruction workflow run in fMRIPrep | — | |
| XCP-D | xcp_d/ |
Functional MRI post-processing and noise regression pipeline | ||
| Quantitative MRI | ||||
| SyMRI | symri/ |
Synthetic image generation | -- | |
| qMRI Postproc | qmri_postproc/ |
Minimal post-processing of SyMRI images | ||
| Diffusion MRI | ||||
| QSIPrep | qsiprep/ |
dMRI data preprocessing pipeline | ||
| QSIRecon | qsirecon-*/ |
dMRI post-processing reconstruction workflows | ||
| MR Spectroscopy | ||||
| OSPREY-BIDS | osprey/ |
MRS data processing pipeline | ||
| EEG | ||||
| HBCD-MADE | made/ |
EEG MADE pipeline adapted for HBCD | ||
| Wearable Sensors | ||||
| HBCD-Motion | motion/ |
Leg movement sensor data processing | ||