GLM Model Doc

Task-fMRI first/second-level GLM remains implemented through nilearn-tool. For tabular formula OLS, robust covariance, Cohen's d, mixed-effects, and prediction baselines, route to the statistical-ml skill.

Overview

GLM refers to the classical General Linear Model used for task-based fMRI activation analysis.

• Model family: non-deep-learning statistical model
• Typical objectives:
  • first-level GLM for subject/session-level task activation analysis
  • second-level GLM for group-level inference across subjects
• Primary input: preprocessed task fMRI, events, TR, optional confounds, optional brain mask
• Primary output: first-level contrast maps, second-level z maps, thresholded activation maps, region-level summaries

In NeuroClaw, this document is model-level guidance for statistical activation workflows rather than phenotype prediction.

Upstream preparation should usually be delegated to:

• fmri-skill for task-fMRI preprocessing and confounds preparation
• nilearn-tool for concrete GLM fitting, design matrix construction, and statistical map generation

Research use only.

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Quick Start

1) Prepare task-fMRI inputs

Expected inputs:

• preprocessed task BOLD image
• events TSV/CSV with onset, duration, trial type
• repetition time (TR)
• optional confounds TSV
• optional mask image

These should be prepared before model fitting. If not ready, delegate to fmri-skill first.

2) Typical first-level GLM flow

Representative operations:

• build design matrix from events and confounds
• fit first-level GLM per subject/session
• compute named contrasts such as task > baseline
• export z maps / effect size maps

Example execution route:

# delegated through claw-shell after preprocessing is confirmed
python skills/nilearn-tool/scripts/task_glm_reference.py \
  --bold path/to/sub-001_task-preproc_bold.nii.gz \
  --events path/to/sub-001_task-events.tsv \
  --confounds path/to/sub-001_confounds.tsv \
  --tr 2.0 \
  --contrast "task-baseline" \
  --output-dir run_models_output/glm/sub-001

3) Second-level GLM (group-level inference)

When multiple subjects are available, use second-level GLM for group-level inference.

Representative operations:

• collect subject-level contrast maps from first-level GLM
• build a group design matrix (for one-sample, two-sample, or covariate models)
• fit a second-level model across subjects
• export group z maps, thresholded figures, and statistical summaries

Typical use cases:

• one-sample group activation inference
• between-group comparison
• covariate-adjusted group analysis (for example age / sex / site)

Example execution route:

# delegated through claw-shell after subject-level contrasts are prepared
python skills/nilearn-tool/scripts/second_level_glm_reference.py \
  --contrast-maps path/to/contrast_map_list.txt \
  --design-matrix path/to/group_design_matrix.csv \
  --contrast group_mean \
  --output-dir run_models_output/glm/group_level

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Input / Output Contract

Required inputs

• preprocessed task fMRI in subject space or standard space
• events table with onset / duration / condition labels
• TR

Optional inputs

• confounds table
• mask image
• subject-level metadata for group models
• first-level contrast maps for second-level GLM
• group design matrix for second-level GLM

Produced outputs

• design matrix figure or CSV snapshot
• first-level beta / contrast / z maps
• thresholded maps and glass-brain figures
• second-level group z maps and statistical summaries

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Recommended Delegation

• preprocessing and task-fMRI preparation -> fmri-skill
• concrete implementation of design matrices and GLM fitting -> nilearn-tool
• shell execution and logging -> claw-shell

Recommended route split:

• first-level GLM -> subject/session-level task activation analysis
• second-level GLM -> group-level inference on first-level contrast maps

No execution before explicit plan confirmation.

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When to Use GLM Instead of Deep Learning

• The user wants classical task activation analysis rather than phenotype prediction.
• The goal is statistical inference on task conditions or contrasts.
• The user wants group-level inference across subjects rather than individual-level prediction.
• Sample size is limited and interpretability of condition effects is more important than representation learning.
• The required output is a contrast map, z map, or cluster-level inference report.

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Limitations and Notes

• GLM is primarily for task-fMRI, not resting-state phenotype modeling.
• Results are sensitive to event timing quality, motion confounds, and preprocessing decisions.
• Group-level inference requires consistent first-level contrast definitions across subjects.
• Second-level GLM requires aligned subject-level maps and a valid group design matrix.

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Reference

• Friston KJ et al. Statistical Parametric Mapping foundations for task-fMRI analysis.
• Nilearn GLM documentation: https://nilearn.github.io/stable/glm/index.html

Created At: 2026-04-14 00:28 HKT Last Updated At: 2026-04-14 00:28 HKT Author: chengwang96