ica

ICA Model Doc

Overview

ICA is a classical non-deep-learning method for resting-state network decomposition.

• Model family: non-deep-learning unsupervised decomposition method
• Typical objectives:
  • identify intrinsic connectivity networks from resting-state fMRI
  • extract spatial component maps and subject-level time series
  • derive component-level connectivity or subject summaries for downstream analysis
• Primary input: preprocessed resting-state fMRI, optional mask, optional group subject list
• Primary output: component maps, subject time series, component loadings, optional connectomes or reports

In NeuroClaw, this document is model-level guidance for ICA-based resting-state decomposition workflows rather than phenotype prediction.

Upstream preparation should usually be delegated to:

• fmri-skill for rs-fMRI preprocessing, nuisance regression, filtering, and standard-space alignment
• nilearn-tool for concrete ICA fitting and component export

Research use only.

Quick Start

1) Prepare resting-state inputs

Expected inputs:

• preprocessed resting-state BOLD images
• optional confounds TSV files
• optional brain mask
• optional subject list or cohort manifest

If these are not ready, delegate to fmri-skill first.

2) ICA route

Representative operations:

• load subject-level or group-level rs-fMRI images
• fit ICA to estimate intrinsic connectivity components
• export component spatial maps and subject time series
• optionally compute component-level correlations

Example execution route:

# delegated through claw-shell after preprocessing is confirmed
python skills/nilearn-tool/scripts/rest_ica_reference.py \
  --input-list path/to/rest_bold_list.txt \
  --mask path/to/group_mask.nii.gz \
  --n-components 20 \
  --output-dir run_models_output/ica

Input / Output Contract

Required inputs

• preprocessed resting-state fMRI in subject space or standard space
• subject list or image list

Optional inputs

• confounds table(s)
• mask image
• repetition time (TR)
• decomposition parameters such as number of components
• group/covariate table for downstream statistical analysis

Produced outputs

• 4D component map image
• subject-level component time series
• component report figures and summary tables
• optional component correlation matrix / connectome

Recommended Delegation

• resting-state preprocessing and denoising -> fmri-skill
• concrete implementation of ICA -> nilearn-tool
• shell execution and logging -> claw-shell

No execution before explicit plan confirmation.

When to Use ICA

• The user wants resting-state network decomposition rather than task activation analysis.
• The goal is to identify intrinsic connectivity networks from rs-fMRI.
• The user wants subject-level component time series for downstream connectivity or clustering.
• Interpretability of spatial networks is more important than supervised phenotype prediction.
• A lightweight classical unsupervised method is preferred over deep learning.

Limitations and Notes

• Results are sensitive to preprocessing quality, head motion, filtering, and masking choices.
• The number of components strongly influences decomposition granularity.
• ICA is unsupervised and does not directly provide statistical group inference.
• Downstream comparisons across groups usually require additional statistical analysis after decomposition.

Reference

• Beckmann CF, Smith SM. Probabilistic independent component analysis for functional magnetic resonance imaging.
• Nilearn decomposition documentation: https://nilearn.github.io/stable/connectivity/resting_state_networks.html

Created At: 2026-04-14 00:31 HKT Last Updated At: 2026-04-14 00:45 HKT Author: chengwang96