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dcm2nii SKILL.md skillA

dcm2nii from cuhk-aim-group/neurodiscovery is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.

Install it, pinned

mdr add cuhk-aim-group/neurodiscovery/dcm2nii@git:20261023.f74c2bd

Pins git:20261023.f74c2bd in mdr.lock. Pin the fingerprint instead.

Audit grade: A, 17 of 17 checks passed
Kind: SKILL.md skill
Repository: cuhk-aim-group/neurodiscovery
Path: skills/dcm2nii/SKILL.md
Versions recorded: 6
Latest version: git:20261023.f74c2bd, committed Oct 23, 2026
First version recorded: Mar 25, 2026
Size: 7,480 bytes
Repository stars: 93
License: MIT

Use this skill whenever the user wants to convert DICOM files or folders to NIfTI format (.nii or .nii.gz), extract neuroimaging volumes from clinical DICOM series (MRI, CT, PET, etc.), prepare raw DICOM data for research processing pipelines, anonymize while converting, or batch-convert multiple series/studies. Triggers include: 'DICOM to NIfTI', 'dcm to nii', 'convert dicom to nii.gz', 'dcm2niix', 'extract nii from dicom', 'batch dicom to nifti', 'prepare dicom for freesurfer/fsl/spm'…

Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.

What the file says

# DICOM to NIfTI conversion

## Overview

DICOM is the universal clinical imaging format containing rich metadata, patient information, acquisition parameters, and often multi-slice series.  
NIfTI (.nii/.nii.gz) is the de-facto standard in neuroimaging research — compact, orientation-aware, and directly supported by FSL, FreeSurfer, SPM, AFNI, ANTs, etc.

This skill wraps `dcm2niix` (latest stable release as of 2026), the most widely used and actively maintained DICOM→NIfTI converter in neuroimaging.  
It produces high-fidelity 3D/4D NIfTI volumes + comprehensive JSON sidecar files containing DICOM tags (BIDS-compatible when using `-b y`).

## Benchmark-Facing Default Mainline

For benchmark-style DICOM conversion tasks, default to the narrow canonical answer instead of a broad converter survey:

- Preferred default command shape: `dcm2niix -z y -b y -o <output_dir> <dicom_dir>`
- For batch conversion, the default answer should be a simple loop over subject/session or series directories.
- Metadata preservation means emitting paired `.nii.gz` and `.json` outputs; present this as the primary validation target.
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add cuhk-aim-group/neurodiscovery/dcm2nii@sha256:9cf5069348f10d35

The line at the top of this page pins the label git:20261023.f74c2bd, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.

Badge

[![mdr](https://markdownregistry.com/badge/art_ovk7khnm6ssgu4k2.svg)](https://markdownregistry.com/a/art_ovk7khnm6ssgu4k2)

3 badge image fetches in 30 days. What the badge shows.

Versions

The registry has recorded 6 versions of this file, between Mar 25, 2026 and Oct 23, 2026, about one every 42 days.

version	committed	commit	size	audit
git:20261023.f74c2bd latest	2026-10-23	f74c2bd	7,480 B	A	view · diff
git:20260506.86420c0	2026-05-06	86420c0	7,474 B	A	view · diff
git:20260505.e9ddd22	2026-05-05	e9ddd22	7,483 B	A	view · diff
git:20260430.becfb09	2026-04-30	becfb09	7,426 B	A	view · diff
git:20260328.891ed93	2026-03-28	891ed93	6,452 B	A	view · diff
git:20260325.72d2cbf	2026-03-25	72d2cbf	6,514 B	A	view

Audit of the latest version

A 17 of 17 checks passed. Fixed automatic checks with no AI involved, so the same checks give the same answer every run.

pass: Frontmatter block present
pass: Frontmatter declares a name
pass: Frontmatter declares a description
pass: Size between 200 bytes and 200 KB (7480 bytes)
pass: No zero-width or bidi control characters
pass: No instruction hidden inside an HTML comment
pass: No link to an exfiltration or paste host
pass: No credential-shaped string
pass: No instruction to send local credentials anywhere
pass: No text hidden with inline styles
pass: No prompt-injection phrasing
pass: No curl or wget piped into a shell
pass: No recursive delete of root, home or parent
pass: No instruction to read or print local credentials
pass: No base64 blob over 200 characters
pass: No link to a raw IP address
pass: No script tag

Source

GitHub

cuhk-aim-group/neurodiscovery · 93 stars · license MIT · pushed 2026-10-23 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_ovk7khnm6ssgu4k2
GET https://markdownregistry.com/api/v1/resolve?ref=cuhk-aim-group/neurodiscovery/dcm2nii
GET https://markdownregistry.com/api/v1/blob/9cf5069348f10d35f2854bcb98bb5d53f5daae01b826680438448108fbebfe91

Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.

Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.