nii2dcm

nii2dcm is a skill for Claude Code, Codex from CUHK-AIM-Group/NeuroClaw. It costs 230 tokens per session (1,583 once invoked), scanned A, original, MIT.

A converter that turns NIfTI brain-imaging files into DICOM image series. NIfTI is common in research, while DICOM is the clinical imaging format used by viewers and hospital systems.

In plain words
What is it for?
Use it to create MRI or swept-volume DICOM series from NIfTI files, transfer metadata from a reference scan, and check the results in tools such as Horos, 3D Slicer, or ITK-Snap.
Why use it?
It makes research-derived images easier to open in clinical imaging software or compare with original scans, while allowing selected metadata to be copied from reference DICOM files.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

Good fit Use it to create MRI or swept-volume DICOM series from NIfTI files, transfer metadata from a reference scan, and check the results in tools such as Horos, 3D Slicer, or ITK-Snap.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/cuhk-aim-group/neuroclaw/nii2dcm
Install

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.

Any agent
npx skills add CUHK-AIM-Group/NeuroClaw --skill nii2dcm
Clone the repo
git clone --depth 1 https://github.com/CUHK-AIM-Group/NeuroClaw

Made for: Claude Code, Codex.

Wrote 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.

agentmods badge for nii2dcm

README.md
[![agentmods](https://agentmods.dev/badge/skills/cuhk-aim-group/neuroclaw/nii2dcm/github.svg)](https://agentmods.dev/skills/cuhk-aim-group/neuroclaw/nii2dcm)
Your own site
<a href="https://agentmods.dev/skills/cuhk-aim-group/neuroclaw/nii2dcm"><img src="https://agentmods.dev/badge/skills/cuhk-aim-group/neuroclaw/nii2dcm/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for nii2dcm

Your own site · 80×15
<a href="https://agentmods.dev/skills/cuhk-aim-group/neuroclaw/nii2dcm"><img src="https://agentmods.dev/badge/skills/cuhk-aim-group/neuroclaw/nii2dcm.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 230 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,583 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector warn 7 Sept 2026
SkillSpector: 3 findings, up to high

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

  • high YARA Match · line 39
    YARA rule matched a known malware signature (reverse shell, backdoor, ransomware, C2 framework, or info stealer).
    Fix: Remove the malware payload or compromised file entirely. Investigate how it entered the skill and audit all other artifacts for additional indicators of compromise.
  • medium MCP Rug Pull · line 62
    Docker image references without a specific tag (:latest is implicit) or digest (@sha256:...) can be silently replaced by a malicious image.
    Fix: Pin the image: image:tag or image@sha256:abc123
  • medium MCP Rug Pull · line 64
    Docker image references without a specific tag (:latest is implicit) or digest (@sha256:...) can be silently replaced by a malicious image.
    Fix: Pin the image: image:tag or image@sha256:abc123
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00230 $0.01583
Opus 5 $0.00115 $0.00792
Sonnet 5 $0.00046 $0.00317
Haiku 4.5 $0.00023 $0.00158

Measured 9d ago against content hash 2d06e9d6e188, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

nii2dcm 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 9d ago.

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.

skills/nii2dcm/SKILL.md · 143 lines

How it starts

The opening of the file, as written. The whole thing — 143 lines — stays where its author put it; the contents beside it link to each section on GitHub.

NIfTI to DICOM conversion

Overview

A NIfTI file (.nii/.nii.gz) is a compact format widely used in neuroimaging research, typically stripped of patient metadata.
DICOM is the clinical standard for medical images, including rich metadata and interoperability with PACS/hospital systems.

This skill wraps nii2dcm (v0.1.6, May 2025) to convert NIfTI volumes into single-frame DICOM series (multi-slice 2D), primarily for MRI-derived data.
It supports modality-specific metadata (MR, SVR) and optional metadata transfer from a reference DICOM file.

Research use only — not certified for clinical diagnosis, treatment, or patient care.

Quick Reference

Task Approach / Command Flag
Basic conversion (generic) nii2dcm input.nii.gz output_dir/
MRI multi-slice series --dicom-type MR or -d MR
SVR (3D swept volume recon) --dicom-type SVR or -d SVR
Copy patient/study metadata --ref-dicom ref.dcm or -r ref.dcm
Custom series description Add via wrapper or post-process
Verify output Open in Horos, 3D Slicer, ITK-Snap

Installation

Via pip (recommended for NeuroClaw)

pip install nii2dcm>=0.1.6
# or latest
pip install git+https://github.com/tomaroberts/nii2dcm.git

From source (for customization / debugging)

git clone https://github.com/tomaroberts/nii2dcm.git
cd nii2dcm
python -m venv venv
source venv/bin/activate
pip install --upgrade pip
pip install -r requirements.txt
pip install .
nii2dcm -h   # Verify

Core dependencies (automatically installed):

  • highdicom >= 0.9.0
  • SimpleITK >= 2.2.0
  • pydicom
  • numpy

Docker alternative (if preferred in containerized env):

docker pull ghcr.io/tomaroberts/nii2dcm:latest
docker tag ghcr.io/tomaroberts/nii2dcm:latest nii2dcm
docker run nii2dcm -v   # check version

Read the full file on GitHub · 143 lines

Changes

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.

  1. 9d ago First seen · 143 lines · 230 tokens per session scan A 2d06e9d6e188

Subscribe to this mod's changes

nii2dcm is a skill published in the GitHub repository CUHK-AIM-Group/NeuroClaw (85 stars, last pushed 6d ago), licensed MIT. It adds 230 tokens to every session and 1,583 once invoked, about $0.0011 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 2026-09-03.

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