dataset
Dataset management operations.
dataset
Section titled “dataset”Usage: nemar dataset [options] [command]
Dataset management
Options: -h, --help display help for command
Commands: ci [dataset-id] Check BIDS validation CI status for the current dataset clone [options] <dataset-id> Clone a dataset from NEMAR collaborators [options] <dataset-id> List collaborators for a dataset commit [options] Stage and commit changes in the current dataset download [options] <dataset-id> Download a dataset from NEMAR or OpenNeuro drop [files...] Free local copies of annexed files (keeps remote copies) get [options] [files...] Download annexed data files for the current dataset help [command] display help for command invite <username> <dataset-id> Invite a user as collaborator to your dataset list [options] List datasets on NEMAR (full catalog) manifest [options] [version] View version manifests for a dataset publish Publication workflow management push [options] Push commits and data to remotes release [options] <dataset-id> Create a version bump PR for a dataset request-access <dataset-id> Request collaborator access to a dataset save [options] Stage and commit changes (alias for commit) search [options] <query> Search datasets using semantic matching status [options] <dataset-id> Check status of a dataset update [options] [path] Push local changes to a dataset via PR upload [options] <path> Upload a BIDS dataset to NEMAR validate [options] [path] Validate a BIDS dataset using the official BIDS validator (requires Deno)
Run with --help-all for examples and detailed descriptions.dataset ci
Section titled “dataset ci”Usage: nemar dataset ci [options] [dataset-id]
Check BIDS validation CI status for the current dataset
Arguments: dataset-id Dataset ID (auto-detected from git remote if omitted)
Options: -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset clone
Section titled “dataset clone”Usage: nemar dataset clone [options] <dataset-id>
Clone a dataset from NEMAR
Arguments: dataset-id Dataset ID (e.g., nm000104)
Options: -o, --output <path> Output directory (default: ./<dataset-id>) -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset collaborators
Section titled “dataset collaborators”Usage: nemar dataset collaborators [options] <dataset-id>
List collaborators for a dataset
Arguments: dataset-id Dataset ID (e.g., nm000104)
Options: --json Output as JSON for scripting -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset commit
Section titled “dataset commit”Usage: nemar dataset commit [options]
Stage and commit changes in the current dataset
Options: -m, --message <msg> Commit message (default: "Save changes") -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset download
Section titled “dataset download”Usage: nemar dataset download [options] <dataset-id>
Download a dataset from NEMAR or OpenNeuro
Arguments: dataset-id Dataset ID (e.g., nm000104 or OpenNeuro ds000248)
Options: -o, --output <path> Output directory (default: ./<dataset-id>) -j, --jobs <number> Parallel download streams (default: 4) (default: "4") --no-data Download metadata only (skip large data files) --resume Resume a partial download into an existing clone --update Pull only the version diff into an existing clone --prune With --update, drop annex objects that no longer exist upstream --subjects <list> Comma-separated subjects (e.g. sub-01,02) --sessions <list> Comma-separated sessions (e.g. ses-pre,post) --tasks <list> Comma-separated tasks (e.g. rest,nback) --runs <list> Comma-separated runs (e.g. 1,2 — matches run-1 and run-01) --datatypes <list> Comma-separated BIDS datatypes (e.g. eeg,emg) --include <globs> Comma-separated extra include globs --exclude <globs> Comma-separated exclude globs (e.g. sourcedata/**) --stimuli Include stimuli/ content (skipped by default; can be large) --derivatives Include derivatives/ content (skipped by default; can be large) --skip-port-check Skip the porting-in-progress check (use if falsely blocked on an OpenNeuro-sourced dataset) -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset drop
Section titled “dataset drop”Usage: nemar dataset drop [options] [files...]
Free local copies of annexed files (keeps remote copies)
Arguments: files Specific files to drop (default: all)
Options: -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset get
Section titled “dataset get”Usage: nemar dataset get [options] [files...]
Download annexed data files for the current dataset
Arguments: files Specific files/paths to get (default: all)
Options: -j, --jobs <number> Parallel download streams (default: "4") --stimuli Include stimuli/ content (skipped by default; can be large) --derivatives Include derivatives/ content (skipped by default; can be large) --skip-port-check Skip the porting-in-progress check (use if falsely blocked on an OpenNeuro-sourced dataset) -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset invite
Section titled “dataset invite”Usage: nemar dataset invite [options] <username> <dataset-id>
Invite a user as collaborator to your dataset
Arguments: username Username to invite dataset-id Dataset ID (e.g., nm000104)
Options: -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset list
Section titled “dataset list”Usage: nemar dataset list [options]
List datasets on NEMAR (full catalog)
Options: --mine List only your datasets (both private and public) --owner <username> List datasets owned by a specific user --search <query> Search by name, description, authors, or tasks --modality <type> Filter by modality (eeg, emg, meg, etc.) --author <name> Filter by author name --task <name> Filter by task name --license <tiers> Filter by license tier(s), comma-separated: public, attribution, sharealike, noncommercial, noderiv, unknown --doi Show only datasets with DOIs --recent [days] Show recently published datasets --sort <order> Sort: newest, oldest, name, participants, size (default: "newest") --json Output as JSON for scripting -n, --limit <n> Results per page (default: 20, max: 200) (default: "20") --page <n> Page number (starts at 1) --offset <n> Skip this many results (alternative to --page) --all Show all results (up to 200) -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset manifest
Section titled “dataset manifest”Usage: nemar dataset manifest [options] [version]
View version manifests for a dataset
Arguments: version Version to view (lists available if omitted)
Options: -d, --dataset <id> Dataset ID (auto-detected from git remote if omitted) --json Output raw JSON -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset publish
Section titled “dataset publish”Usage: nemar dataset publish [options] [command]
Publication workflow management
Options: -h, --help display help for command
Commands: help [command] display help for command request <dataset-id> Request publication of a dataset resend <dataset-id> Resend publication request notification to admins status <dataset-id> Check publication status of a datasetdataset publish request
Section titled “dataset publish request”Usage: nemar dataset publish request [options] <dataset-id>
Request publication of a dataset
Arguments: dataset-id Dataset ID (e.g., nm000104)
Options: -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset publish resend
Section titled “dataset publish resend”Usage: nemar dataset publish resend [options] <dataset-id>
Resend publication request notification to admins
Arguments: dataset-id Dataset ID (e.g., nm000104)
Options: -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset publish status
Section titled “dataset publish status”Usage: nemar dataset publish status [options] <dataset-id>
Check publication status of a dataset
Arguments: dataset-id Dataset ID (e.g., nm000104)
Options: -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset push
Section titled “dataset push”Usage: nemar dataset push [options]
Push commits and data to remotes
Options: -j, --jobs <number> Parallel upload streams for S3 (default: "4") --no-s3 Skip pushing data to S3 remote --pr Create a pull request after pushing -t, --title <title> Pull request title (with --pr) -b, --body <body> Pull request body (with --pr) -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset release
Section titled “dataset release”Usage: nemar dataset release [options] <dataset-id>
Create a version bump PR for a dataset
Arguments: dataset-id Dataset ID (e.g., nm000104)
Options: --type <type> Bump type: patch, minor, or major --version <version> Explicit version (e.g., 2.0.0) --dir <path> Use existing local clone instead of cloning --monitor Watch CI checks and offer to merge -y, --yes Skip confirmation and proceed -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset request-access
Section titled “dataset request-access”Usage: nemar dataset request-access [options] <dataset-id>
Request collaborator access to a dataset
Arguments: dataset-id Dataset ID (e.g., nm000104)
Options: -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset save
Section titled “dataset save”Usage: nemar dataset save [options]
Stage and commit changes (alias for commit)
Options: -m, --message <msg> Commit message (default: "Save changes") -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset search
Section titled “dataset search”Usage: nemar dataset search [options] <query>
Search datasets using semantic matching
Options: --modality <type> Filter by modality (eeg, emg, meg, etc.) --json Output as JSON for scripting --limit <n> Limit results (default: 20) (default: "20") -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset status
Section titled “dataset status”Usage: nemar dataset status [options] <dataset-id>
Check status of a dataset
Arguments: dataset-id Dataset ID (e.g., nm000104)
Options: --json Output as JSON for scripting -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset update
Section titled “dataset update”Usage: nemar dataset update [options] [path]
Push local changes to a dataset via PR
Arguments: path Path to local dataset clone (default: current directory)
Options: --bump <type> Version bump type: patch, minor, or major (default: "patch") --branch <name> Custom branch name -m, --message <msg> Commit message --monitor Watch CI checks and offer to merge -y, --yes Skip confirmation and proceed -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset upload
Section titled “dataset upload”Usage: nemar dataset upload [options] <path>
Upload a BIDS dataset to NEMAR
Arguments: path Path to BIDS dataset directory
Options: -n, --name <name> Dataset name (defaults to BIDS Name, then directory name) -d, --description <desc> Dataset description --skip-validation Skip BIDS validation (not recommended) --skip-orcid Skip co-author ORCID collection --dry-run Show what would be uploaded without doing it -j, --jobs <number> Parallel upload streams (default: 4) (default: "4") -y, --yes Skip confirmation and proceed --restart Clear upload progress and re-upload all files --no Skip confirmation and decline -h, --help display help for command
Run with --help-all for examples and detailed descriptions.dataset validate
Section titled “dataset validate”Usage: nemar dataset validate [options] [path]
Validate a BIDS dataset using the official BIDS validator (requires Deno)
Arguments: path Path to BIDS dataset directory (default: ".")
Options: --ignore-warnings Only report errors, not warnings -c, --config <file> Validation config file (.bidsvalidatorrc) -r, --recursive Validate derivatives subdirectories --prune Skip sourcedata and derivatives for faster validation -v, --verbose Show verbose output --json Output results as JSON (for scripting) --version-info Show BIDS validator version info --update Force update the BIDS validator to the latest version -h, --help display help for command
Run with --help-all for examples and detailed descriptions.