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Components
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NiChart is designed to integrate independent image processing and analysis pipelines. The following sections detail these pipelines.

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Current Pipelines
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These pipelines are currently active and accessible within the NiChart Project

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1. sMRI Biomarkers of Disease and Aging
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Neuroimaging pipeline for computing AI biomarkers of disease and aging from T1-weighted MRI scans. The pipeline applies the following steps for processign and analysis.

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Segmentation
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`DLMUSE <https://neuroimagingchart.com/components/#Image%20Processing>`_: Rapid and accurate **brain anatomy segmentation**

.. image:: https://github.com/CBICA/NiChart_Project/blob/031d1cafc5091eb514511ee25af189d5f0b5ac56/resources/images/dlicv%2Bdlmuse_segmask.png
   :alt: DLMUSE

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Harmonization
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`COMBAT <https://neuroimagingchart.com/components/#Harmonization>`_: **Statistical data harmonization** of ROI volumes to `reference data <https://neuroimagingchart.com/components/#Reference%20Dataset>`_

.. image:: https://raw.githubusercontent.com/CBICA/NiChart_Project/refs/heads/ge-dev/resources/images/combat_agetrend.png
   :alt: COMBAT

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Supervised ML Biomarkers
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`SPARE-AD and SPARE-Age indices <https://neuroimagingchart.com/components/##Machine%20Learning%20Models>`_: AI biomarkers of **Alzheimer's Disease and Aging** related brain atrophy patterns

.. image:: https://raw.githubusercontent.com/CBICA/NiChart_Project/refs/heads/ge-dev/resources/images/sparead%2Bage.png
  :alt: SPARE-AD and SPARE-Age indices

`SPARE-CVR indices <https://alz-journals.onlinelibrary.wiley.com/doi/abs/10.1002/alz.067709>`_: AI biomarkers of brain atrophy patterns associated with **Cardio-Vascular Risk Factors**

.. image:: https://raw.githubusercontent.com/CBICA/NiChart_Project/refs/heads/ge-dev/resources/images/sparecvr.png
  :alt: SPARE-CVR indices, Govindarajan, S.T., et. al., Nature Communications, 2024

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Semi-supervised ML Biomarkers
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 - `SurrealGAN indices <https://www.nature.com/articles/d41586-024-02692-z>`_: Data-driven phenotyping of brain aging, **5 Brain Aging Subtypes**

.. image:: https://raw.githubusercontent.com/CBICA/NiChart_Project/refs/heads/ge-dev/resources/images/sgan1.jpg
   :alt: SurrrealGAN indices

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2. WM Lesion Segmentation
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Neuroimaging pipeline for segmenting white matter lesions on FLAIR MRI scans.

`DLWMLS <https://neuroimagingchart.com/components/#Image%20Processing>`_: Rapid and accurate **white matter lesion segmentation**

.. image:: https://github.com/CBICA/NiChart_Project/blob/031d1cafc5091eb514511ee25af189d5f0b5ac56/resources/images/dlwmls.png
   :target https://github.com/CBICA/NiChart_DLWMLS
   :alt: DLWMLS

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Under Development
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These pipelines are planned for integration in future NiChart releases.

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1. DTI Biomarkers of Disease and Aging
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2. fMRI Biomarkers of Disease and Aging
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3. CCL-NMF: Dynamic Patterns of Brain Aging from Coupled Cross-sectional and Longitudinal Non-negative Matrix Factorization
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