# NiDB Documentation

## NiDB Documentation

- [NeuroInformatics Database](https://docs.neuroinfodb.org/nidb/neuroinformatics-database.md)
- [HIPAA Compliance](https://docs.neuroinfodb.org/nidb/neuroinformatics-database/hipaa-compliance.md): NiDB's HIPAA compliance
- [Installation](https://docs.neuroinfodb.org/nidb/getting-started/installation.md): Detailed installation instructions
- [Quick Install](https://docs.neuroinfodb.org/nidb/getting-started/installation/quick-install.md)
- [Changing data paths](https://docs.neuroinfodb.org/nidb/getting-started/installation/changing-data-paths.md)
- [How to change passwords](https://docs.neuroinfodb.org/nidb/getting-started/installation/how-to-change-passwords.md)
- [Optional software](https://docs.neuroinfodb.org/nidb/getting-started/installation/optional-software.md): List of extremely useful, but optional, software to help when using NiDB
- [MySQL/MariaDB tweaks](https://docs.neuroinfodb.org/nidb/getting-started/installation/mysql-mariadb-tweaks.md): Performance changes for large databases
- [Upgrade](https://docs.neuroinfodb.org/nidb/getting-started/upgrade.md): Detailed upgrade instructions
- [Quick Upgrade](https://docs.neuroinfodb.org/nidb/getting-started/upgrade/quick-upgrade.md)
- [Migrate Existing Installation](https://docs.neuroinfodb.org/nidb/getting-started/upgrade/migrate-existing-installation.md): How to migrate an existing NiDB installation to a new server
- [User's Guide](https://docs.neuroinfodb.org/nidb/using-nidb/users-guide.md)
- [Importing data](https://docs.neuroinfodb.org/nidb/using-nidb/users-guide/importing-data.md)
- [Managing data](https://docs.neuroinfodb.org/nidb/using-nidb/users-guide/managing-data.md): This section describes how to manage meta data and imaging data files for subjects enrolled in projects.
- [Finding & exporting data](https://docs.neuroinfodb.org/nidb/using-nidb/users-guide/finding-and-exporting-data.md)
- [Managing projects](https://docs.neuroinfodb.org/nidb/using-nidb/users-guide/managing-projects.md)
- [Pipelines & analysis](https://docs.neuroinfodb.org/nidb/using-nidb/users-guide/pipelines-and-analysis.md)
- [Calendar](https://docs.neuroinfodb.org/nidb/using-nidb/users-guide/calendar.md): Calendar for appointments, scheduling of equipment time, etc
- [Administration](https://docs.neuroinfodb.org/nidb/using-nidb/administration.md)
- [Front end (user facing)](https://docs.neuroinfodb.org/nidb/using-nidb/administration/front-end-user-facing.md): Front end settings are what the users see. Projects, users, etc.
- [Back end](https://docs.neuroinfodb.org/nidb/using-nidb/administration/back-end.md): Back end are all settings and configuration that keep NiDB running
- [nidb command line](https://docs.neuroinfodb.org/nidb/using-nidb/administration/nidb-command-line.md): Command line usage of nidb
- [Data Storage Hierarchy](https://docs.neuroinfodb.org/nidb/specifications/data-storage-hierarchy.md)
- [DICOM Anonymization](https://docs.neuroinfodb.org/nidb/specifications/dicom-anonymization.md): DICOM Anonymization Levels
- [Working with Imaging Data](https://docs.neuroinfodb.org/nidb/tutorials/working-with-imaging-data.md)
- [Exporting BIDS format](https://docs.neuroinfodb.org/nidb/tutorials/working-with-imaging-data/exporting-bids-format.md)
- [Uploading data for a sample project](https://docs.neuroinfodb.org/nidb/tutorials/working-with-imaging-data/uploading-data-for-a-sample-project.md): How to upload data into a sample project
- [Troubleshooting Missing Imaging Data](https://docs.neuroinfodb.org/nidb/tutorials/working-with-imaging-data/troubleshooting-missing-imaging-data.md): It's not supposed to happen... but it can. Here's how to fix it.
- [Import DICOM data](https://docs.neuroinfodb.org/nidb/tutorials/working-with-imaging-data/import-dicom-data.md): Tutorial on how to import DICOM data into NiDB
- [MR scan quality control](https://docs.neuroinfodb.org/nidb/tutorials/working-with-imaging-data/mr-scan-quality-control.md): MR scans quality parameters
- [Manipulating Subjects, Studies, & Series](https://docs.neuroinfodb.org/nidb/tutorials/manipulating-subjects-studies-and-series.md): Various tutorials on how to fix data
- [Working with subject IDs](https://docs.neuroinfodb.org/nidb/tutorials/manipulating-subjects-studies-and-series/working-with-subject-ids.md): This tutorial describes how to find subjects by ID, and how to map multiple IDs.
- [Renaming series](https://docs.neuroinfodb.org/nidb/tutorials/manipulating-subjects-studies-and-series/renaming-series.md)
- [Pipelines](https://docs.neuroinfodb.org/nidb/tutorials/pipelines.md): Various pipeline tutorials
- [Working with Redcap](https://docs.neuroinfodb.org/nidb/tutorials/working-with-redcap.md): Tutorials regarding Redcap
- [Importing Data from a Redcap Project](https://docs.neuroinfodb.org/nidb/tutorials/working-with-redcap/importing-data-from-a-redcap-project.md): Tutorial on how to import data form a Redcap project to a NiDB project
- [Importing Subjects from Redcap](https://docs.neuroinfodb.org/nidb/tutorials/working-with-redcap/importing-subjects-from-redcap.md): Tutorial on how to import subjects form Redcap
- [Reports based on data imported from Redcap](https://docs.neuroinfodb.org/nidb/tutorials/working-with-redcap/reports-based-on-data-imported-from-redcap.md): Tutorial on how to create a report using Redcap data
- [Analysis Builder](https://docs.neuroinfodb.org/nidb/tutorials/analysis-builder.md): Tutorial on how to create reports using Analysis Builder
- [Administration of Users, Projects, & System](https://docs.neuroinfodb.org/nidb/tutorials/administration-of-users-projects-and-system.md)
- [User Permissions](https://docs.neuroinfodb.org/nidb/tutorials/administration-of-users-projects-and-system/user-permissions.md)
- [Creating new projects](https://docs.neuroinfodb.org/nidb/tutorials/administration-of-users-projects-and-system/creating-new-projects.md)
- [Adding Users to Projects](https://docs.neuroinfodb.org/nidb/tutorials/administration-of-users-projects-and-system/adding-users-to-projects.md)
- [Editing the config file](https://docs.neuroinfodb.org/nidb/tutorials/administration-of-users-projects-and-system/editing-the-config-file.md)
- [Deleting all the data](https://docs.neuroinfodb.org/nidb/tutorials/administration-of-users-projects-and-system/deleting-all-the-data.md): This tutorial describes how to completely erase all data from an NiDB installation
- [Squirrel data sharing format](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format.md)
- [squirrel utilities](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/squirrel-utilities.md): The squirrel command line program
- [Using the squirrel library](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/using-the-squirrel-library.md): Overview of how to use the squirrel C++ library
- [Example package](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/example-package.md)
- [squirrel vs BIDS](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/squirrel-vs-bids.md): Understanding the differences between package formats
- [Specification v1.0](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0.md): Format specification for v1.0
- [Package root](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/package-root.md): JSON object
- [package](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/package.md): JSON object
- [data](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/data.md): JSON object
- [subjects](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/data/subjects.md): JSON array
- [studies](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/data/subjects/studies.md): JSON array
- [series](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/data/subjects/studies/series.md): JSON array
- [params](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/data/subjects/studies/series/params.md): Separate JSON file - params.json
- [analysis](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/data/subjects/studies/analysis.md): JSON array
- [observations](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/data/subjects/observations.md): JSON array
- [interventions](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/data/subjects/interventions.md): JSON array
- [group-analysis](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/data/group-analysis.md): JSON array
- [pipelines](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/pipelines.md): JSON array
- [data-steps](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/pipelines/data-steps.md): JSON array
- [Pipeline scripts](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/pipelines/pipeline-scripts.md): Details about how pipeline scripts are formatted for squirrel and NiDB
- [experiments](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/experiments.md): JSON array
- [data-dictionary](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/data-dictionary.md): JSON object
- [Modalities](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/modalities.md)
- [JSON full listing](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/specification-v1.0/json-full-listing.md): Full listing of JSON fields in alphbetical order
- [Building squirrel library and utils](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/building-squirrel-library-and-utils.md)
- [Building Python Wrapper](https://docs.neuroinfodb.org/nidb/contribute/squirrel-data-sharing-format/building-squirrel-library-and-utils/building-python-wrapper.md): How to build a Python wrapper for the squirrel library
- [Building NiDB](https://docs.neuroinfodb.org/nidb/contribute/building-nidb.md): How to build NiDB and contribute to its development
- [Creating a Development VM](https://docs.neuroinfodb.org/nidb/contribute/creating-a-development-vm.md): This describes how to create a Linux virtual machine to build NiDB


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