Abide skill

ABIDE Skill (Dataset-Orchestration Layer)

Overview

abide-skill is the NeuroClaw orchestration skill for the ABIDE (Autism Brain Imaging Data Exchange) dataset.

It coordinates a fixed three-phase workflow:

1. Download ABIDE data from the FCP/INDI repository or NITRC.
2. Prepare and validate BIDS-style data organization for downstream processing.
3. Delegate modality pipelines to smri-skill and fmri-skill.

It also provides phenotype extraction and QC integration paths:

• Extract and merge ABIDE phenotype tables (diagnosis, age, sex, site, FIQ, ADOS, etc.).
• Generate per-subject QC summaries with exclusion lists.

This skill follows NeuroClaw hierarchy:

• Defines WHAT to do, not low-level implementation details.
• Does not execute direct shell commands itself.
• Delegates all execution via claw-shell to base/tool skills.

Research use only.

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Download Stage (Mandatory First Step)

Source

ABIDE data is distributed through the FCP/INDI repository:

• ABIDE I: https://fcon_1000.projects.nitrc.org/indi/abide/
• ABIDE II: https://fcon_1000.projects.nitrc.org/indi/abide_II.html
• NITRC mirror: https://www.nitrc.org/projects/fcp_indi/

Supported ABIDE Data Packages

• ABIDE I: 1,112 subjects from 17 international sites (539 ASD, 573 controls)
• ABIDE II: 1,044 subjects from 19 sites
• Phenotype data: CSV files with demographics, diagnosis, cognitive scores
• Preprocessed derivatives (optional): CPAC, DPARSF, CCS, NeuroMark pipelines

Delegation Rules for Download

• Environment/setup checks: dependency-planner + conda-env-manager
• Download tool installation and execution: claw-shell
• Optional raw-data organization to BIDS-style staging: bids-organizer

Download Inputs to Confirm in Plan

• Target ABIDE version (I, II, or both)
• Target subset (full cohort, specific sites, or ASD/control only)
• Subject list scope (full or custom IDs)
• Whether to download raw data or preprocessed derivatives
• Destination directory with sufficient disk space

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Narrow Path: ABIDE Raw NIfTI -> BIDS Staging

Use this path when the task only asks to reorganize raw ABIDE NIfTI files into a BIDS-style dataset and does not require preprocessing, ROI extraction, phenotype merging, or downstream analysis.

When this narrow path should dominate

• The task objective is limited to ABIDE NIfTI staging, BIDS renaming, sidecar handling, and dataset-level metadata.
• Inputs are already local ABIDE NIfTI files or ABIDE-style subject/site folders.
• The required deliverable is a direct staging script or command sequence, not a plan for fMRIPrep or downstream analysis.

Narrow-path contract

• Do not widen the solution to fMRIPrep, ROI extraction, phenotype merging, or downstream analysis unless the task explicitly requires them.
• Treat this as a direct file-organization problem: scan ABIDE subject/site layout, normalize subject labels, map modalities to BIDS names, copy or symlink NIfTI plus matching sidecars, and write dataset-level metadata plus staging logs.
• If the task is benchmark-style, prefer a single direct end-to-end staging script over a confirmation-first orchestration plan.

Expected narrow-path behavior

1. Detect ABIDE-style subject IDs (numeric, e.g., 0050642) and normalize to BIDS labels such as sub-0050642.
2. Detect site information and encode as BIDS session or metadata (e.g., ses-NYU, or site column in participants.tsv).
3. Route modalities:
   • T1w -> anat/*_T1w
   • rs-fMRI/BOLD -> func/*_task-rest_bold
4. Preserve or rename matching JSON sidecars when available; if metadata is absent, create only the minimal dataset files required by the task and log the limitation.
5. Emit dataset-level outputs such as dataset_description.json, participants.tsv, README, and a manifest or skipped-file report.

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Core Workflow (Never Bypassed)

1. Identify user target: full ABIDE download, imaging subset, phenotype extraction, or BIDS staging only.
2. Generate a numbered plan with tools, outputs, runtime, storage, and risks.
3. Wait for explicit confirmation (YES / execute / proceed).
4. On confirmation, run download stage first (if needed).
5. After download success, run BIDS preparation using scripts/reorganize_abide.py.
6. Delegate to modality skills:
   • smri-skill for structural MRI (T1w)
   • fmri-skill for resting-state fMRI (rs-fMRI)
7. If phenotype extraction is requested, run scripts/extract_abide_phenotype.py.
8. If QC summary is requested, run scripts/abide_qc_summary.py.
9. Save outputs into an ABIDE-centered structure under abide_output/.

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Input Layout (Example)

Subject 0050642 from site NYU:

abide_raw/
  NYU/
    0050642/
      session_1/
        anat_1/
          anat.nii.gz
        func_1/
          func.nii.gz
  phenotype/
    ABIDE_phenotypic.csv

Or flat layout:

abide_raw/
  0050642/
    anat/
      T1w.nii.gz
    func/
      rest_bold.nii.gz

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BIDS Preparation

Script: scripts/reorganize_abide.py

Converts ABIDE raw directory structure to BIDS-compliant layout.

python skills/abide-skill/scripts/reorganize_abide.py \
  --input /path/to/abide_raw \
  --output /path/to/abide_bids \
  --phenotype /path/to/abide_raw/phenotype/ABIDE_phenotypic.csv

Features:

• Subject ID normalization: numeric ABIDE IDs to BIDS sub-NNNNNNN
• Site extraction and encoding in participants.tsv
• Modality routing: T1w, rs-fMRI
• Sidecar JSON preservation and validation
• dataset_description.json and participants.tsv generation with phenotype metadata
• Dry-run mode: --dry-run to preview without copying

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Multimodal Processing Delegation

After BIDS staging completes, abide-skill delegates by modality:

Modality	Delegated skill	Typical tasks	Main outputs
sMRI (T1w)	smri-skill	brain extraction, tissue segmentation, cortical reconstruction, ROI morphometry	smri_output/ derivatives and stats
rs-fMRI	fmri-skill	preprocessing, denoising, ROI time series, connectivity	fmri_output/ derivatives, timeseries, connectivity

Delegation Strategy

• If user asks for full ABIDE analysis: run sMRI -> fMRI in ordered phases.
• If user asks for one modality only: call only the corresponding modality skill.
• If compute resources are adequate and the user approves parallel runs: run modality pipelines in parallel.

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Phenotype Extraction

Script: scripts/extract_abide_phenotype.py

Extracts and merges ABIDE phenotype tables for downstream analysis.

python skills/abide-skill/scripts/extract_abide_phenotype.py \
  --phenotype-dir /path/to/abide_raw/phenotype \
  --output /path/to/abide_output/phenotype/merged_phenotype.csv \
  --columns subject,DX_GROUP,AGE_AT_SCAN,SEX,FIQ,VIQ,PIQ,site \
  --imaging-ids /path/to/abide_output/bids/participants.tsv

Features:

• Reads ABIDE phenotype CSV files (ABIDE I and II compatible)
• Standardizes column names (DX_GROUP: 1=ASD, 2=control)
• Column selection and renaming
• Site encoding and grouping
• Missing value handling
• Cross-reference with imaging subject list
• Outputs merged CSV ready for statistical analysis or model training

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QC Integration

Script: scripts/abide_qc_summary.py

Generates per-subject QC summaries and exclusion lists.

python skills/abide-skill/scripts/abide_qc_summary.py \
  --fmriprep-dir /path/to/abide_output/fmriprep \
  --freesurfer-dir /path/to/abide_output/smri/freesurfer \
  --raw-qc /path/to/abide_raw/phenotype/ABIDE_phenotypic.csv \
  --output /path/to/abide_output/qc/qc_summary.csv \
  --exclude-output /path/to/abide_output/qc/exclude_list.csv \
  --fd-threshold 0.3 \
  --coverage-threshold 0.8

Features:

• Reads fMRIPrep confounds (framewise displacement, DVARS)
• Reads FreeSurfer recon-all QC metrics
• Incorporates ABIDE QC flags (QC_RATER_1, func_perc_fd, anat_rater_1, etc.)
• Applies exclusion criteria: motion threshold (FD), coverage threshold, structural quality
• Per-site QC summary for site-effect assessment
• Outputs per-subject QC summary CSV and exclusion list CSV

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Recommended Output Layout

All assets should be organized under ./abide_output/:

• abide_output/raw/ (downloaded original ABIDE files)
• abide_output/bids/ (staged BIDS data)
• abide_output/staging/ (optional normalized staging intermediate)
• abide_output/smri/ (links or copies from smri_output/)
• abide_output/fmri/ (links or copies from fmri_output/)
• abide_output/phenotype/ (merged phenotype tables)
• abide_output/qc/ (QC summaries and exclusion lists)
• abide_output/logs/ (download + orchestration logs)

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Benchmark Adapter Guidance

For benchmark-style prompts, do not force the full download -> staging -> multimodal processing orchestration when the task is only asking for local ABIDE data staging or organization.

• If the task starts from raw ABIDE data already present on disk and only asks for BIDS-style staging / organization:
  • skip the mandatory download stage
  • do not automatically delegate to smri-skill or fmri-skill
  • default to the narrow path local raw ABIDE discovery -> BIDS-style staging -> minimal metadata -> validation/report
• In benchmark mode, do not require explicit confirmation before presenting the direct staging solution.
• Preserve the ABIDE-centered output contract under abide_output/bids/ when the task is specifically a staging benchmark.
• Only use the full multimodal orchestration and confirmation-heavy workflow when the prompt explicitly asks for download, end-to-end ABIDE processing, or post-staging structural / functional analysis.

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Safety and Execution Policy

• No execution before explicit plan confirmation.
• All execution must be routed via claw-shell.
• Missing dependencies must be resolved by dependency-planner before running.
• If download fails for partial subjects, continue batch with clear failure report and retry list.

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Important Notes and Limitations

• ABIDE data from different sites may have varying acquisition parameters; site effects should be accounted for in analysis.
• ABIDE subject IDs are numeric and vary in length across sites.
• ABIDE I and II have different phenotype table formats; the extraction script handles both.
• ABIDE provides preprocessed derivatives from multiple pipelines (CPAC, DPARSF, CCS); raw data processing via fMRIPrep is recommended for reproducibility.
• ABIDE data does not include task-fMRI; only resting-state fMRI is available.
• abide-skill is orchestration-only; detailed preprocessing logic remains in smri-skill and fmri-skill.

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When to Call This Skill

• User asks for end-to-end ABIDE workflow.
• User asks to download ABIDE data and then run sMRI/rs-fMRI processing.
• User needs BIDS staging for raw ABIDE NIfTI files.
• User asks to extract and merge ABIDE phenotype tables.
• User asks for ABIDE-specific QC summaries and exclusion lists.
• User needs a single entry point for ABIDE multimodal orchestration.

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Complementary / Related Skills

• smri-skill
• fmri-skill
• bids-organizer
• fmriprep-tool
• freesurfer-tool
• neurostorm
• brain_gnn
• dependency-planner
• conda-env-manager
• claw-shell

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Reference

• ABIDE I: https://fcon_1000.projects.nitrc.org/indi/abide/
• ABIDE II: https://fcon_1000.projects.nitrc.org/indi/abide_II.html
• Di Martino et al., 2014, The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism
• BIDS spec: https://bids.neuroimaging.io/

Created At: 2026-05-06 01:45 HKT Last Updated At: 2026-05-06 01:45 HKT Author: chengwang96