dcm2nii skillA
dcm2nii is agent-read markdown (skill) from cuhk-aim-group/neurodiscovery: 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', 'anonym.
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns 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
mdr add cuhk-aim-group/neurodiscovery/dcm2nii@git:20260506.86420c0mdr add cuhk-aim-group/neurodiscovery/dcm2nii@sha256:69bd022783129e36Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_ovk7khnm6ssgu4k2)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260506.86420c0 latest | 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
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (7474 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
cuhk-aim-group/neurodiscovery · 91 stars · license MIT · pushed 2026-09-22 · 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/69bd022783129e3624a2c6d44ba470a4a2087f8a088ca1eea183b533a718f5ea
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