openjdata/neuroj repository overview

   # print help information and flags
   docker run openjdata/neuroj:v2025

   # preview commands (dry-run, does not execute) to convert a database (including all included datasets) to JSON
   docker run openjdata/neuroj:v2025 neuroj -i /path/to/database/rootfolder -o /path/to/output/json/folder -db openneuro

   # convert a database (a collection of datasets) to JSON in batch with 12 parallel threads (1 thread per dataset)
   docker run openjdata/neuroj:v2025 neuroj -i /path/to/database/rootfolder -o /path/to/output/json/folder -db openneuro --convert -t 12

   # convert a single dataset (including all files under sub-folders) to JSON in parallel (1 thread per file)
   docker run openjdata/neuroj:v2025 neuroj -i /path/to/database/rootfolder -o /path/to/output/json/folder -db openneuro -ds ds000001 --convert

   # convert a database to JSON, assuming the last segment of the input path as database name
   docker run openjdata/neuroj:v2025 neuroj -i /path/to/database/databasename -o /path/to/output/json/folder

   # convert a single dataset ds000001 to JSON (dry-run only, add --convert to run)
   docker run openjdata/neuroj:v2025 neuroj -i /path/to/database/databasename -o /path/to/output/json/folder -ds ds000001

   # convert all datasets under openneuro to JSON using 30 parallel threads, processing 30 files in parallel
   docker run openjdata/neuroj:v2025 neuroj -i /path/to/database/rootfolder -o /path/to/output/json/folder -db openneuro -ds \\* --convert -t 30

   # once dataset.json files are converted in the output folder, push all .json files to NeuroJSON.io (admin only)
   docker run openjdata/neuroj:v2025 neuroj -o /path/to/output/json/folder -db openneuro --push -n

   # upload /path/to/output/json/folder/ds000005.json to neurojson.io:7777/openneuro database
   docker run openjdata/neuroj:v2025 neuroj -o /path/to/output/json/folder -db openneuro -ds ds000005 --push -n

   # list all databases currently hosted on NeuroJSON.io
   docker run openjdata/neuroj:v2025 neuroj --list

   # list all databases currently hosted on NeuroJSON.io, format the output with jq
   docker run openjdata/neuroj:v2025 neuroj --list | jq '.'

   # list all datasets stored under the 'openneuro' database
   docker run openjdata/neuroj:v2025 neuroj --list -db openneuro

   # list all datasets strored under the 'openneuro' database and print all datasets using jq filters
   neuroj --list -db openneuro | jq '.rows[] | .id'

   # query server-level information of the database openneuro (return dataset count, file sizes etc)
   docker run openjdata/neuroj:v2025 neuroj --info -db openneuro

   # search the IDs of the first 10 (limit:10) datasets in the openneuro database starting from the 3rd (skip:2) datasets
   docker run openjdata/neuroj:v2025 neuroj -db openneuro --find '{"selector":{},"fields":["_id"],"limit":10,"skip":2}'

   # query the dataset name "_id" and "dataset_description.json" records of the first two datasets in "openneuro" and format with jq
   docker run openjdata/neuroj:v2025 neuroj -db openneuro --find '{"selector":{},"fields":["_id","dataset_description\\\\.json"],"limit":2}' | jq '.'

    # set default external link URL template
    export NJPREP_FALLBACK_URL="https://neurojson.org/io/stat.cgi?action=get&db=%DB%&doc=%DS%"

    # convert all datasets in a database to JSON
    docker run openjdata/neuroj:v2025 njprep /database/root/ /output/json/root/ database_name

    # convert a specific dataset "dataset_name" in a specific database to JSON
    docker run openjdata/neuroj:v2025 njprep /database/root/ /output/json/root/ database_name dataset_name

    # convert a single file or subject-folder in a given database and dataset
    docker run openjdata/neuroj:v2025 njprep /database/root/ /output/json/root/ database_name dataset_name /path/to/a/file