Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add instructions/christiangaser/t1prep/claude-mdgit clone --depth 1 https://github.com/ChristianGaser/T1PrepWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/instructions/christiangaser/t1prep/claude-md)<a href="https://agentmods.dev/instructions/christiangaser/t1prep/claude-md"><img src="https://agentmods.dev/badge/instructions/christiangaser/t1prep/claude-md.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.01598 | $0.01598 |
| Opus 5 | $0.00799 | $0.00799 |
| Sonnet 5 | $0.00320 | $0.00320 |
| Haiku 4.5 | $0.00160 | $0.00160 |
Grade A, and why
T1Prep CLAUDE.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured today.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 139 lines — stays where its author put it; the contents beside it link to each section on GitHub.
CLAUDE.md – T1Prep Project
For full contributor documentation see Agents.md.
Sub-Agent Routing Rules
- Always sequential: All tasks (security, performance, style, refactoring) must be processed sequentially.
- No parallelization: Only one sub-agent or one check may be active at a time.
- Workflow: First execute
security, thenperformance, thenstyle. Wait for each step to complete. - Dependencies: B tasks must wait for the output of A tasks.
Background Execution Rules
Run in background automatically:
- Web research and documentation lookups
- Codebase exploration and analysis
- Security audits and performance profiling
- Any task where results aren't immediately needed
- Research or analysis tasks (not file modifications)
- Results aren't blocking your current work
Overview
T1Prep is a Python-based pipeline for preprocessing and segmenting T1-weighted MRI data (bias-field correction, segmentation, lesion detection, cortical surface reconstruction, CAT12 integration). Code lives in src/, helper/dev scripts in scripts/, Flask web UI in src/t1prep/webui/.
Entry points are installed into the environment's bin/ (the canonical way to
run T1Prep): T1Prep (bash orchestrator), PyCAT (symlink to T1Prep; same
CLI, PyCAT startup banner), t1prep-ui, t1prep-run (Python
single-subject), CAT_SurfView, CAT_VolView, t1prep-make-apps, t1prep-download-models, t1prep-bbreg. The
scripts/ folder
is a source-tree/dev fallback and should not be put on PATH.
Key Commands
# CLI (from <venv>/bin on PATH; or ./scripts/T1Prep in a source checkout)
T1Prep --help
T1Prep --out-dir /tmp/out file.nii.gz
# Python API
from t1prep import run_t1prep
# Web UI
t1prep-ui --port 5050
# Sanity check
python -m compileall src
# Tests
pytest
# Recalibrate the QA rating bounds from a processed BrainWeb Phantom set
python scripts/qa_calibrate.py /path/to/BWP/report
# Score the spherical registration against the Mindboggle-101 manual labels
python scripts/eval_mindboggle.py project --mindboggle DIR... --t1prep DIR --work DIR
python scripts/eval_mindboggle.py dice --work DIR --protocol both
# Linting / formatting
black src scripts
flake8 src scripts # or: ruff check src scripts
shellcheck scripts/*.sh
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- today Changed · +4 lines · +65 tokens per session 82372ffac46a
- 4d ago First seen · 135 lines · 1,533 tokens per session scan A cc1ab39171fc
T1Prep CLAUDE.md is an instructions file published in the GitHub repository ChristianGaser/T1Prep (10 stars, last pushed yesterday), licensed Apache-2.0. It adds 1,598 tokens to every session, about $0.0080 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
Other instructions, from other repositories
vscode buildNext.instructions.md
Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).
spec-kit AGENTS.md
AGENTS.md instructions for github/spec-kit, covering agents.md, about spec kit and specify, quickstart — add a new integration in 5 steps, integration architecture and integrationmanifest — file tracking.
codex AGENTS.md
AGENTS.md instructions for openai/codex, covering rust/codex-rs, the codex-core crate, code review rules, crate api surface and model visible context.
langchain AGENTS.md
AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, applying the notice (cutover) and fallback chain (never fail the build).
next.js AGENTS.md
Instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.