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xnatctl

Use when running xnatctl commands, writing scripts that call xnatctl, troubleshooting XNAT CLI operations, or helping users with XNAT neuroimaging server administration via the command line. Triggers on mentions of xnatctl, XNAT CLI, session download/upload, prearchive, scan management, or XNAT project administration.

install
source · Clone the upstream repo
git clone https://github.com/rickyltwong/xnatctl
Claude Code · Install into ~/.claude/skills/
git clone --depth=1 https://github.com/rickyltwong/xnatctl ~/.claude/skills/rickyltwong-xnatctl-xnatctl
manifest: SKILL.md
source content

xnatctl CLI Reference

Modern CLI for XNAT neuroimaging server administration. Resource-centric commands with consistent output formats, parallel operations, and profile-based configuration.

Command Hierarchy

xnatctl
  config    init | show | use-context | current-context | add-profile | remove-profile
  auth      login | logout | status | test
  project   list | show | create
  subject   list | show | rename | delete
  session   list | show | download | upload | upload-exam
  scan      list | show | delete | download
  resource  list | show | upload | download
  prearchive list | archive | delete | rebuild | move
  pipeline  list | run | status | jobs | cancel
  admin     refresh-catalogs | user add | audit
  dicom     validate | inspect | list-tags | anonymize   (requires xnatctl[dicom])
  api       get | post | put | delete                    (raw REST escape hatch)
  whoami
  health ping
  completion [bash|zsh|fish]

Global Options (all commands)

FlagShortDescription
--profile
-p
Named profile from config
--output
-o
json
or 
table
(default: table)
--quiet
-q
IDs only output
--verbose
-v
Debug logging

Parent-Resource Options (session & scan commands)

FlagShortPurposeKey Rule
--project
-P
Project IDEnables label lookup for -E
--subject
-S
Subject ID/labelUsed in 
session list
(filter) and 
session upload
--experiment
-E
Experiment ID or labelLabels require -P (explicit or via profile 
default_project
)

Critical: 

-E LABEL
without 
-P
fails. 
-E XNAT_E00001
(accession ID) works without 
-P
.

Quick Reference: Common Commands

Setup & Auth

# Initialize config with profile
xnatctl config init --url https://xnat.example.org --profile myserver

# Add another profile
xnatctl config add-profile prod --url https://prod.xnat.org --project DEFAULT_PROJ

# Switch profiles
xnatctl config use-context prod

# Login (prompts for credentials if not in config/env)
xnatctl auth login -p myserver

# Test connection
xnatctl auth test

Projects & Subjects

# List projects
xnatctl project list

# Show project details
xnatctl project show MYPROJ

# List subjects with filter (NOTE: colon syntax, not equals)
xnatctl subject list -P MYPROJ --filter "label:CTRL_*"

# Delete subject (with safety)
xnatctl subject delete SUB001 -P MYPROJ --dry-run
xnatctl subject delete SUB001 -P MYPROJ --yes

Sessions

# List sessions in project
xnatctl session list -P MYPROJ

# Show session (by label - needs -P)
xnatctl session show -P MYPROJ -E MR_Session_01

# Show session (by accession ID - no -P needed)
xnatctl session show -E XNAT_E00001

# Download session - single ZIP (default)
xnatctl session download -P MYPROJ -E MR_Session_01 --out ./data

# Download session - parallel per-scan (workers > 1)
xnatctl session download -P MYPROJ -E MR_Session_01 --out ./data -w 8

Uploads

# Upload DICOM directory (parallel batches)
xnatctl session upload ./dicoms -P NEURO -S SUB001 -E SESS001 --workers 4

# Upload DICOM archive file
xnatctl session upload ./archive.tar -P NEURO -S SUB001 -E SESS001

# Gradual per-file upload (parallel)
xnatctl session upload ./dicoms -P NEURO -S SUB001 -E SESS001 --gradual --workers 16

# Upload exam root (DICOM + resources)
# Directory structure: top-level dirs become resources, DICOMs found recursively
xnatctl session upload-exam ./exam_root -P NEURO -S SUB001 -E SESS001 -w 4

# Attach resources only (skip DICOM upload)
xnatctl session upload-exam ./exam_root -P NEURO -S SUB001 -E SESS001 --attach-only

upload vs upload-exam: 

upload
handles DICOM files only. 
upload-exam
handles a mixed directory (DICOMs + non-DICOM resource files like PDFs, spreadsheets). In upload-exam, top-level directories become session-level resources by name.

Scans

# List scans
xnatctl scan list -E XNAT_E00001

# Delete specific scans (comma-separated with -s flag)
xnatctl scan delete -E XNAT_E00042 -P BRAIN -s 1,3,5 --dry-run
xnatctl scan delete -E XNAT_E00042 -P BRAIN -s 1,3,5 --yes

# Delete ALL scans
xnatctl scan delete -E XNAT_E00042 -s "*" --yes

# Download scans as ZIP
xnatctl scan download -E XNAT_E00001 -s 1,2,3 --out ./scans

Resources

# List resources on session
xnatctl resource list XNAT_E00001

# List resources on scan
xnatctl resource list XNAT_E00001 --scan 1

# Upload file/directory as resource
xnatctl resource upload XNAT_E00001 MY_RESOURCE ./data/

# Download resource
xnatctl resource download XNAT_E00001 MY_RESOURCE --file ./output.zip

Prearchive

Note: Prearchive commands use POSITIONAL args: 

PROJECT TIMESTAMP SESSION_NAME

# List prearchive sessions
xnatctl prearchive list
xnatctl prearchive list --project MYPROJ

# Archive (move to main archive)
xnatctl prearchive archive MYPROJ 20240115_143022 SessionFolder

# Delete from prearchive
xnatctl prearchive delete MYPROJ 20240115_143022 SessionFolder --yes

# Rebuild (refresh metadata)
xnatctl prearchive rebuild MYPROJ 20240115_143022 SessionFolder

# Move to different project
xnatctl prearchive move MYPROJ 20240115_143022 SessionFolder TARGET_PROJ

Pipelines

# List pipelines
xnatctl pipeline list --project MYPROJ

# Run pipeline and wait for completion
xnatctl pipeline run dcm2niix -e XNAT_E00001 -P key1=val1 -P key2=val2 --wait

# Check job status (with watch mode)
xnatctl pipeline status JOB_ID --watch

# Cancel job
xnatctl pipeline cancel JOB_ID --yes

Admin

# Refresh catalogs with parallel workers
xnatctl admin refresh-catalogs MYPROJ -O checksum -O populateStats --parallel --workers 8

# Add user to project groups
xnatctl admin user add jsmith Owners --projects MYPROJ

# View audit log
xnatctl admin audit -P MYPROJ --since 7d --limit 50

Raw API (escape hatch)

# GET with query parameters (use -P key=value, NOT query strings in path)
xnatctl api get /data/projects/MYPROJ/subjects -P format=json

# POST with data
xnatctl api post /data/projects -d '{"ID":"NEW_PROJ","name":"New Project"}'

# DELETE with confirmation skip
xnatctl api delete /data/experiments/XNAT_E00001 --yes

DICOM Tools (requires 
xnatctl[dicom]
)

# Validate DICOM files
xnatctl dicom validate ./dicoms -r

# Inspect headers
xnatctl dicom inspect ./scan.dcm -t PatientID -t Modality

# Anonymize
xnatctl dicom anonymize ./input ./output --patient-id ANON001 --remove-private -r

Configuration

Config file: 

~/.config/xnatctl/config.yaml

default_profile: default
output_format: table
profiles:
  default:
    url: https://xnat.example.org
    verify_ssl: true
    timeout: 21600       # 6 hours (default for large transfers)
    default_project: MYPROJ
    username: admin      # optional
    password: secret     # optional

Environment variables (priority: CLI args > env vars > profile > prompt):

VariablePurpose
XNAT_TOKEN
Session token (highest auth priority, skips credential prompt)
XNAT_URL
Server URL (auto-creates 
default
profile)
XNAT_USER
Username
XNAT_PASS
Password
XNAT_PROFILE
Active profile
XNAT_VERIFY_SSL
true
/
false
XNAT_TIMEOUT
Timeout seconds

Gotchas

  1. -o
    is output FORMAT     (
    json
    /
    table
    ), NOT output directory. Use 
    --out
    for download destination.
  2. Filter uses colon: 
    --filter "label:CTRL_*"
    not 
    label=CTRL_*
    .
  3. Scan IDs use 
    -s
    flag    : 
    -s 1,3,5
    (comma-separated) or 
    -s "*"
    (all). NOT positional args.
  4. Prearchive uses positional args: 
    PROJECT TIMESTAMP SESSION_NAME
    . NOT 
    -P
    /
    -E
    flags.
  5. API params use 
    -P key=value
    : NOT query strings appended to path.
  6. Workers flag varies: session download uses 
    -w
    , upload uses 
    --workers
    . Both control parallelism.
  7. -P
    flag is overloaded    : In session/scan commands, 
    -P
    means 
    --project
    . In 
    api
    and 
    pipeline
    commands, 
    -P
    means parameter (
    key=value
    ). Context matters.
  8. Default timeout is 6 hours (21600s) for large DICOM transfers.
  9. upload-exam waits for archive: By default waits for XNAT to finish archiving before attaching resources. Control with 
    --wait-for-archive
    /
    --no-wait-for-archive
    .
  10. default_project
    fallback    : If profile has 
    default_project
    , 
    -P
    can be omitted and session/scan commands auto-resolve.

Safety Decorators

Destructive commands include 

--yes/-y
(skip confirmation) and 
--dry-run
(preview only). Always use 
--dry-run
first for delete/rename operations.

Parallel commands include 

--parallel/--no-parallel
and 
--workers N
.