The QC scan quality control table can be download as ".csv" file by clicking "Save As CSV" button at the end of the MR QC table.

NiDB can be built on most RedHat compatiable Linux distributions. Download the Rocky 8 or 9 DVD ISO from https://rockylinux.org/download/

Create a VM in VMWare Workstation Player

Start VMWare Workstation Player, click Create a New Virtual Machine. Choose the ISO image that you downloaded. Click Next.

Select the Guest OS and version; in this example Linux and RHEL 9. Click Next.

Give your VM a meaningful name and location. Click Next.

Choose the disk size and format. 30GB is preferable and choose Store virtual disk as a single file. Click Next.

Click Customize Hardware... and change the VM hardware. If you have extra cores available on your host machine, 4 or more cores is preferable. Same with memory, if you have extra memorty available on your host machine, 8GB or more memory is preferable. When done, click Close.

Click Finish.

On the main VMWare interface, double click your new VM to start it.

Installing Linux

Install RHEL compatible with the Server with GUI install option. Disable SELinux. Make sure to enable the network and assign a hostname. Also helpful to create a user and assign them root permissions.

System (Back end) Administration

Settings that the end-user will not see

• NiDB Settings

• Informational Links

• Backup

• Modules

• Modalities

• Sites

• Instances

• Mass email

• DICOM receiver

Special Config Variables

Some variables can only be changed by editing the config file directly and cannot be changed from the NiDB settings page.

offline - Set to 1 if the website should be unavailable to users, 0 for normal access. Default is 0

debug - Set to 1 if the website should print out every SQL statement, and other debug information. Default is 0

hideerrors - Set to 1 if the website should hide SQL errors from the user. 0 otherwise. Default is 0

• .rpm based installation for RHEL 8 and RHEL 9 compatible (not for CentOS Stream)

• Store any neuroimaging data, including MR, CT, EEG, ET, Video, Task, GSR, Consent, MEG, TMS, and more

• Store any assessment data (paper-based tasks)

• Store clinical trial information (manage data across multiple days & dose times, etc)

• Built-in DICOM receiver. Send DICOM data from PACS or MRI directly to NiDB

• Bulk import of imaging data

• User and project based permissions, with project admin roles

• Search and manipulate data from subjects across projects

• Automated imaging analysis pipeline system

• "Mini-pipeline" module to process behavioral data files (extract timings)

• All stored data is searchable. Combine results from pipelines, QC output, behavioral data, and more in one searchable

• Export data to NFS, FTP, Web download, NDA (NIMH Data Archive format), or export to a remote NiDB server

• Export to squirrel format

• Project level checklists for imaging data

• Automated motion correction and other QC for MRI data

• Calendar for scheduling equipment and rooms

• Usage reports, audits, tape backup module

• Intuitive, modern UI. Easy to use

Features

.rpm based installation & upgrade

Install or upgrade NiDB in minutes on RHEL compatible Linux OS.

Automated import of DICOM data

DICOM data can be automatically imported using the included dcmrcv DICOM receiver. Setup your MRI or other DICOM compatible device to send images to NiDB, and NiDB will automatically archive them. Image series can arrive on NiDB in any order: partial series, or full series to overlap incomplete series.

Store any type of data

Literally any type of imaging data: binary; assessment; paper based; genetics. See full list of supported modalities. All data is stored in a hierarchy: Subject --> Study --> Series. Data is searchable across project and across subject.

Store clinical trial data

NiDB stores multiple time-points with identifiers for clinical trials; exact day numbers (days 1, 15, 30 ...) or ordinal timepoints (timepoint 1, 2, 3 ...) or both (day1-time1, day1-time2, day2-time1, ... )

Bulk import of imaging data

Got a batch of DICOMs from a collaborator, or from an old DVD? Import them easily

Search and export imaging data

Find imaging data from any project (that you have permissions to...) and export data. Search by dozens of criteria.

Export to multiple formats

Image formats

• Original raw data - DICOM, Par/Rec, Nifti

  • Anonymized DICOM data: partial and full anonymization

• Nifti3d

• Nifti3dgz

• Nifti4d

• Nifti4dgz

• squirrel

Package formats

• squirrel

• BIDS

• NDA/NDAR

Destinations

• NFS share

• Web

• Public download/dataset

• Local FTP

• Remote NiDB instance

Search and export non-imaging data

Data obtained from pipeline analysis, imported and locally generated measures, drugs, vitals, measures, are all searchable.

Full analysis pipeline system

From raw data to analyzed, and storing result values/images. Utilize a compute cluster to process jobs in parallel. Example below, 200,000 hrs of compute time completed in a few weeks. Hundreds of thousands of result values automatically stored in NiDB and are searchable.

Automated MR quality control

Large number of automatically generated metrics. Metrics are exportable as .csv and tables.

Calendar

Fully featured calendar, running securely on your internal network. Repeating appts, blocking appts, and time requests.

Publications

• Book GA, Anderson BM, Stevens MC, Glahn DC, Assaf M, Pearlson GD. Neuroinformatics Database (NiDB)--a modular, portable database for the storage, analysis, and sharing of neuroimaging data. Neuroinformatics. 2013 Oct;11(4):495-505. doi: 10.1007/s12021-013-9194-1. PMID: 23912507; PMCID: PMC3864015. https://pubmed.ncbi.nlm.nih.gov/23912507/

• Book GA, Stevens MC, Assaf M, Glahn DC, Pearlson GD. Neuroimaging data sharing on the neuroinformatics database platform. Neuroimage. 2016 Jan 1;124(Pt B):1089-1092. doi: 10.1016/j.neuroimage.2015.04.022. Epub 2015 Apr 16. PMID: 25888923; PMCID: PMC4608854. https://pubmed.ncbi.nlm.nih.gov/25888923/

Outdated information Watch an overview of the main features of NiDB (recorded 2015, so it's a little outdated): Part 1 | Part 2 | Part 3

Documentation

Getting Started

Using NiDB

Advanced

Directory structure

Files associated with this section are stored in the following directory. subjectID, studyNum, seriesNum are the actual subject ID, study number, and series number. For example /data/S1234ABC/1/1.

/data/<SubjectID>/<StudyNum>/<SeriesNum>/params.json

Single study, single pipeline

This configuration starts off with a single imaging study, and a single pipeline. An example is a single T1 image which is passed through a freesurfer pipeline.

Here's a sample pipeline specification for the above scenario

Pipeline: Data & Scripts - Options Pipeline dependency --> Criteria: study

Pipeline: Data & Scripts - Data: T1 --> Output --> Data Source: Study

Single study, multiple pipeline

This configuration gets data from a single imaging study, but passed it through one or more pipelines. An example is an fMRI task that requires structural processing as in the HCP pipeline: the fMRI stats require output from a freesurfer pipeline.

Pipeline A: Data & Scripts - Options Pipeline dependency --> Criteria: study

Pipeline A: Data & Scripts - Data Output --> Data Source: Study

Pipeline B: Data & Scripts - Options Pipeline dependency --> dependency: pipeline A Pipeline dependency --> Criteria: study

Multiple study, single pipeline

This configuration takes data from multiple studies and passes it through a single pipeline. An example is an fMRI task analysis that requires a T1 from a different study. The T1 comes from study A, and the fMRI task from study B.

In this example, Study1 is the 'study of record'. All analyses, statuses, and results are associated with Study1. Here's the pipeline settings to use in this example.

Pipeline A - "Preprocessing1" Data & Scripts tab: Options --> Pipeline dependency --> Criteria: study Data (fMRI) --> Output --> Data Source: Study Data (T1) --> Output --> Data Source: Subject Data (T1) --> Output --> Subject linkage: Nearest in time

Pipeline B - "Stats1" Data & Scripts tab: Options --> Pipeline dependency --> dependency: pipeline A Options --> Pipeline dependency --> Criteria: study

Multiple study, multiple pipeline

This configuration takes data from multiple studies and uses multiple pipelines to analyze the data. This can come in multiple ways. Below are some examples of complex pipelines.

In this example, the pipeline settings are the same as above. The only difference is that each analysis (each study) will pull fMRI from the study, and the T1 from 'somewhere'. For the studies that have a T1, it will come from there. For studies that don't have a T1, the T1 will come from the study nearest in time.

Here's the pipeline settings to use in this example.

Pipeline A - "Preprocessing1" Data & Scripts tab: Options --> Pipeline dependency --> Criteria: study Data (fMRI) --> Output --> Data Source: Study Data (T1) --> Output --> Data Source: Subject Data (T1) --> Output --> Subject linkage: Nearest in time

Pipeline B - "Stats1" Data & Scripts tab: Options --> Pipeline dependency --> dependency: pipeline A Options --> Pipeline dependency --> Criteria: study

Rename the series(s) and click Rename.

The series(s) will now be renamed.

Renaming non-MR series

Click the protocol name for the series, and an edit box will appear. Edit the protocol (series name) and press enter.

Example

Suppose we have subject S1234ABC. This subject has one study, and ten series in that study. We'd expect to see the following on the website for subject S1234BC study 2.

But, we go to export the data through the search page or through a pipeline, and not all of the series have data! If we look on the disk, we see there are series missing.

That's not good. This could also appear as though all series directories do exist, but if we dig deeper, we find that the dicom directory for each series is missing or empty. So, where's the data? We have to do some detective work.

Let's look around the subject's directory on the disk.

That's interesting, there appears to be another directory. Our study is 2, but there's also a study 1, and it doesn't show up on the NiDB website. Maybe our data is in there? Let's look.

That looks like our data! We can verify by doing a diff between directories that exist in both studies.

If this is the data we are looking for, we can copy all of the data from study 1 to study 2.

After the copying is done, you should be able to go back to the study page, and click the View file list button at the bottom and see all of expected series.

Install NiDB

1. Download the latest .rpm package

2. yum --nogpgcheck localinstall nidb-xxxx.xx.xx-1.el8.x86_64.rpm

3. Secure the MariaDB installation by running sudo mysql_secure_installation and using the following responses

1. Finish Setup - Use Firefox to view http://localhost/setup.php . Follow instructions on the page to configure the server

   • The setup page must be accessed from localhost -or- the config file must be manually edited to include the IP address of the computer you are using the access setup.php.

   • Edit /nidb/nidb.cfg and add your IP address (comma separated list) to the [setupips] config variable. It should look something like [setupips] 127.0.0.1, 192.168.0.1 depending on the IP(s)

PHP Variables

PHP has default resource limits, which may cause issues with NiDB. Limits are increased during the installation/upgrade of NiDB. The current limits are listed on the bottom of the Settings page as a reference if your NiDB installation is not working as expected.

cron

NiDB replaces the crontab for the nidb account with a list of modules required to run NiDB. This crontab is cleared and re-setup with the default nidb crontab each time NiDB is setup/upgraded. Any items you add to the crontab will be erased during an upgrade and need to be setup again.

System messages

At the top of the Settings page, you can specify messages which are displayed system-wide when a user logs in. These can be messages related to planned system down time or other notifications.

Informational Links

NiDB is often run on a network with many other websites such as compute node status, internal Wikis, and project documentation. Links to websites can be specified on the Admin page directly.

Backup

Depending on the size or importance of your data, you may want to backup your data in an off-line format rather than simply mirroring the hard drives onto another server. A backup system is available to permanently archive imaging data onto magnetic tape. LTO tapes are written in triplicate to prevent loss of data. Each tape can be stored in a separate location and data integrity ensured with a majority rules approach to data validation.

Backup process

Backup directory paths are specified in the config file. See the Config variables section.

Data is automatically copied to the backupdir when it is written to the archivedir. Data older than 24 hours is moved from backupdir to backupstagingdir. When backupstagingdir is at least the size of backupsize, then a tape is ready to be written.

Tape 0 lists the current size of the backupstagingdir.

Modules

NiDB has several modules that control backend operations. These can be enabled, disabled, put into debug mode, and the logs viewed.

Enabled modules are listed in green. Running modules will list the process id of the instance of the module. Some modules can have multiple instances running, ie multithreaded, while some modules can only run 1 instance. Each running instance is color-coded with green having checked in recently and red having checked in 2 hours.

Each module has lock file(s) stored in /nidb/lock and log files in /nidb/logs

Module manager

The module manager monitors modules to see if they have crashed, and restarts them if they have. If a module does not checkin within 2 hours (except for the backup module) it is assumed that it has crashed, and the module manager will reset the module by deleting the lock file and removing the database entry.

Modalities

Each modality requires it's own SQL table. Details of the SQL tables, including number of rows and table size, can be viewed on the modalities page.

Sites

Sites are used in various places within NiDB. This section is used when data is collected at multiple sites and stores details about each site.

Instances

NiDB has the ability to separate projects into different instances, basically creating project groups, to which access permissions can be applied. For example, a user can be part of certain instances, giving them the opportunity to view projects within that instance if they have permissions. This can be a good way to group projects from a multi-site project.

Mass email

This will attempt to send an email to every registered email address within the system. It's spam, so use it sparingly.

DICOM receiver

Step 2

Fill the following information for API connection to Redcap

• Redcap Server: Name of the redcap server

• Redcap Token: An API token provided by Redcap administrator.

• Redcap Event: The name of the redcap event that stores the subject's information.

Step 3

Provide the following redcap field names.

• Record ID (Required): Actual Redcap field name for Redcap record id.

• Alternate ID (Optional): Name of the redcap field holding subject id other than record id, if any:

• First Name (Required): Redcap field name containing the first name information. This is not the actual first name of a subject.

• Last Name (Required): Field name containing the last name information in Redcap. This is not the actual last name of a subject.

• Birthdate (Required): Redcap field name storing the date of birth information for the subjects.

• Sex (Required): Redcap field name that stores the sex of the subjects. For this field, codes stored in Redcap representing the subject's sex should be provided here. The codes for male (M), and female(F) are required. Codes for Other (O) and undefined (U) can also be defined if used in the Redcap project. A suggestive coding scheme 1 for male (M), 2 for female (F), 3 for other (O) and 4 for undefined (U) is also displayed for help.

Step 4

After providing the required information regarding the Redcap fields click Subjects Information button.

If all the above information is correct, then the list of the subjects from redcap will be shown as follows:

Step 5

There can be four types of subjects in the list. Those are:

1. Ready to Import: are the one those are in redcap and can be imported.

2. Found in an other project: these are present in another project under inthe NiDB database. They can also be imported, but need to be selected to get import.

3. Processing: these are already in the process of being imported and cannot be selected to import.

4. Already exist in the project: these already exist in the current project and cannot be duplicated.

After selecting the desired subjects to import, click Import Selected Subjects to start the import process.

Enroll in Project

In the enrollments section, select the project you want to enroll in, and click Enroll. The subject will now be enrolled in the project. Permissions within NiDB are determined by the project, which is in theory associated with an IRB approved protocol. If a subject is not enrolled in a project, the default is to have no permissions to view or edit the subject. Now that the subject is part of a project, you will have permissions to edit the subject's details. Once enrolled, you can edit the enrollment details and create studies.

Once you've fill out the information, click Add and the project will be created. No users will have permissions to access this project. Follow the Adding Users to Projects to add user permissions.

Related articles

• Front-end administration

• Adding users to projects

Directory structure

Files associated with this section are stored in the following directory, where <GroupAnalysisName> is the name of the analysis.

/group-analysis/<GroupAnalysisName>/

1. From a project's main page click Analysis Builder. The above interface is used to produce reports in Analysis Builder.

2. Select the variables to generate the report.

3. As we are generating report based on the data that is imported from Redcap, the following variables cudit1, cudit2, cudit_3... are selected which were mapped as an example in the tutorial Importing Data from Redcap Project.

4. There are various setting that can be set to generate a report, more details on this in in the Tutorial on Analysis Builder. After the appropriate setting is selected, Press Update Summary button.

5. The report similar to the one shown in the figure below will be displayed.

6. Select the output format as .csv if the data is needed to store in a csv file format.

A complex report with more parameters involve can also be created. An Example of such report is available in the tutorial about Analysis Builder.

Directory structure

Files associated with this section are stored in the following directory. Where ExperimentName is the unique name of the experiment.

/experiments/<ExperimentName>

data-dictionary

data-dictionary-item

group-analysis

experiments

interventions

observations

package

pipelines

series

studies

subjects

Data types

The JSON specification includes several data types, but squirrel uses some derivative data types: string, number, date, datetime, char. Date, datetime, and char are stored as the JSON string datatype and should be enclosed in double quotes.

Directory Structure

The JSON file squirrel.json is stored in the root directory. A directory called data contains any data described in the JSON file. Files can be of any type, with file any extension. Because of the broad range of environments in which squirrel files are used, filenames must only contain alphanumeric characters. Filenames cannot contain special characters or spaces and must be less than 255 characters in length.

Squirrel Package

A squirrel package becomes a package once the entire directory structure is combined into a zip file. The compression level does not matter, as long as the file is a .zip archive. Once created, this package can be distributed to other instances of NiDB, squirrel readers, or simply unzipped and manually extracted. Packages can be created manually or exported using NiDB or squirrel converters.

Package Specification

FSL

FSL is required for MRI QC modules. FSL requires at least 20GB free disk space to install. Download FSL from https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation and follow the installation instructions. After installation, note the location of FSL, usually /usr/local/fsl.

Alternatively, try these commands to install FSL

firejail

firejail is used to run user-defined scripts in a sandboxed environment. This may be deprecated in future releases of NiDB. Install firejail from https://firejail.wordpress.com/

Install NiDB rpm

Download the latest .rpm package from https://github.com/gbook/nidb/release and run the following commands

Secure the MariaDB installation by running mysql_secure_installation as root and using the following responses. The MariaDB root password is already set to password.

Finish Setup

Use Firefox to view http://localhost/setup.php (or http://servername/setup.php). Follow the instructions on the webpage to configure the server.

1 - Backup SQL database

Copy the mysqldump command and run that on the command line. It should create a .sql file that contains a backup of the database. This is required even for new installations because you should become familiar with, and get int the habit of, backing up the SQL database. After you've backed up the database using mysqldump, refresh the setup page and it should allow you to continue with the setup.

Click Next to continue, and the following page will show the status of Linux packages required by NiDB.

2 - Linux Prerequisites

If there are any missing packages or if a version needs to be updated, it will show here. Install the package and refresh the page. Click Next to continue, and the following page will show the SQL schema upgrade information.

3 - Database connection

Enter the MariaDB root password, which should be password if this is the first installation. The SQL schema will be upgraded using the .sql file listed at the bottom. As your instance of NiDB collects more data, the tables can get very large and tables over 100 million rows are possible. This will cause the setup webpage to time out, so there is an option to skip tables that have more than x rows. This should really only be done if a specific table is preventing the schema upgrade because it so large and you are familiar with how to manually update the schema. The debug option is available to test the upgrade without actually changing the table structure. Click Next to continue, and the following page will perform the actual schema upgrade.

4 - Schema upgrade

If any errors occur during upgrade, they will be displayed at the bottom of the page. You can attempt to fix these, or preferably seek help on the NiDB github support page! Click the red box to dismiss any error messages. Click Next to go to the next page which will show the configuration variables.

5 - Config settings

On this page you can edit variables, paths, name of the instance, email configuration, enable features.

Click Write Config to continue.

The locations of the written config file(s) are noted on this page. nidb-cluster.cfg is meant to be placed on cluster nodes, to allow nidb pipelines running on the cluster to communicate with the main nidb instance and perform check-ins and storing of pipeline results.

Setup should now be complete and you can visit the home page.

Creating Users

NIS Users

NiDB will check by default if an NIS account already exists when a user logs in for the first time. If the user exists in NIS, an account will created within NiDB. NIS must be enabled and able to authenticate to the NIS through the NiDB server.

Regular Users

To create a regular user, go to Admin → Users. Click the Add User button. Enter their information, including password and email address. The username can be any field, such as an alphanumeric string, or an email address. If the user is given NiDB admin permissions, then they will be able to add/edit users.

Account Self-registration

On public servers, or systems where users are allowed to register themselves, they can create an account and verify their email address to fully register the account. The account will then exist, but they will have no permissions to any projects within NiDB. After a user registers, they will appear on the Admin → Users → All Other Users tab. Click the username to edit their project permissions. Note: be careful allowing users to self-register, for obvious reasons.

Managing Users

There are 3 options of where to find users A) users in the current instance (switch instance by clicking the instance list in the upper left menu) B) users not in the current instance C) deleted users

To manage project permissions for users, go to Admin → Users and click on the username you want to manage. The page can change the name, password, email, admin status, if the account is enabled/disabled, and the projects to which the user has permissions. After changing any information on the page, click the Save button at the bottom of the page. See list of user options and settings below.

Projects

Data collected in the system must be associated with a subject, and that subject must be enrolled in a project. There is a default project in NiDB called Generic Project, but its preferable to create projects parallel to IRB approved studies.

Projects are listed after clicking on the Admin → Projects menu. Clicking the project allows editing of the project options. Clicking the Create Project button will show the new project form. Fill out the form, or edit the form, using the following descriptions of the options

Reports

Reports of imaging studies (often used for billing/accounting purposes on MRI equipment for example) are organized by modality or equipment. Clicking any of the 'year' links will display a calendar for that year with the number of studies per day matching the specified criteria. Clicking the month name will show a report for that month and modality/equipment. Clicking the day will show a report of studies collected on that day.

The following page with the option "Create Project" will appear. This page also contains a list of all the current projects. To create a new project, click on the "Create Project" button on the left corner of the screen as shown in the figure below.

On the next page, fill the following form related to the new project. Name the new project, fill the project number. Select the option "Use Custom IDs" if project need to use its own ID system. Select the Principal Investigator (PI) and project administrator (PA) from the existing NiDB users. The PI and PA can be the same subject. Mention the start and end date if they are known. Also there is an option if you want to copy an existing setting from one of your projects.

After clicking "Add" button, a new project will be added to the project list and it will be shown in the list of existing projects as shown in the figure below.

Project Setup

To setup the project for collecting data click the name of the project on the above page and the following page can be used to add the right set of protocols.

After adding the required set of protocols, a list of protocols will be shown as follow. A protocol can be deleted by clicking the "delete" button in front of an added protocol as shown in the figure below.

To define a protocol, click on the name of a protocol in the above list. For example if we click on EEG-Rest, the following page will appear with the existing list of EEG-series being already used in various projects. You can pick any of those to add to your own protocol group. A group name can be assigned by using the "Protocol group name" box at the end of the page as shown. After clicking the "Add" button the selected series in the group will be added to the group and will be shown on the right.

Working With a Project

After setting up project accordingly, the project can be accessed by users having its rights. A user can access a project via "Projects" menu from the main menu. A list of existing projects will be displayed. TO search a specific project, type the name of a project and the list will reduced to the projects containing the search phrase.

Click the name of the project from the list as shown above. A project specific page will appear as seen below.

A project page consists of some information regarding the current project. Under the project name there is total number of subjects and studies. Undeneath that is a message box consists of number of studies. One can dismiss this message box by clicking "dismiss" button or view all the studies inside the message box.

In the middle of a project page is "Data Views" for subjects, studies, checklist for subjects and an option to QC the MR scans.

To update information regarding the subjects in the current project, click on the "Subjects" button in the data view, a page will appear where the information can be updated for all the subjects and can be saved at once by clicking "Save" button at the end.

By clicking the Studies button from Data Views section, following page will appear. The studies can be selected to perform various operations like adding enrollment tags, moving studies to another project.

Checklist provides a brief summary on the subjects, studies and their status as shown below.

On the right side of the project page is a star that can be selected to make this project "favorite" that will show this project on the main page of NiDB to access it easily from there. Also there are links to the project related tools and their settings. This section is named as "Project tools & settings". This section includes:

• Data Dictionary

• Analysis Builder

• Study Templates

• BIDS Protocol Mapping

• NDA Mapping

• Behavioral Minipipelines

• Recap-> NiDB Transfer

• Reset MRI QA

It also possess the parameters required to connect this project remotely.

The last section of a project page consists of a list of subjects registtered, with its alternate Ids, GUID, DOB, Sex, and status as shown below:

The projects main-menu also has a sub-menu to navigate through various project related tools. The sub-menu includes links to Data Dictionary, Assessments, Subjects, Studies, Checklist, MR Scan QC, Behavioral pipeline and Templates. Also "Project List" can navigate back to the list of all the projects in the current database instance.

In the next section the steps to create two reports are listed showing how various options can be employed to create a desired report.

Building Reports

Analysis builder is designed to create reports based on variables that can be selected from different types of measures, and modalities shown in the Analysis Builder interface screen above. This includes modalities like MR, EEG, cognitive and biological measurements.

Simple Report

Following are the steps to create a simple report where data is not grouped and there is no drug / dose variable is used. The following figure shows the selection of variables and settings to generate this report.

Steps - Simple Report

1. To generate a report, select a project from the dropdown menu at the top of the screen.

2. Select the variables for any one or combination of modalities and measures. We chose four cognitive variables those are imported from Redcap.

3. Choose if you want to group data on the base of date, or measure. We are not selecting this option for the simple report.

4. The output of a report can be control by various option like:

   • Selection of all subjects data regardless of their data presence

   • What should be displayed for a blank and missing values

   • Inclusion of, event duration, time, date, subject's height, weight and date of birth

5. Select the output format of the report, showing it on the screen or saving it as csv file.

6. Hit the Update Summary button to generate the final report as shown on the right section of the screen below.

Repeated Measures Report

This is a report that involve the variables which are repetitive in nature. Also we want the variables to display with respect to the drug administered time. Analysis Builder will automatically create variables that holds the time since dose information.

For this type of report, usually time repeated measure are reported, but other measures may be added if desired.

Steps - Repeated Measure Report

1. Select a project from the dropdown list of projects on the top of Analysis Builder interface.

2. Choose the variables to display in this report. As mentioned above this is a repetitive measures report, so the variables that are repetitive in nature; collected multiple times in a day and on multiple days are selected. These include measure from MRI and biological data. Also these variables are collected before or after administration of drug.

3. To include the drug / dose information on this report, select the drug related variable as shown in the above figure in green rectangle. Different drug dose was administrated on three different days, and all three days were selected.

4. The time since dose variables shall be calculated and displayed if the option Include Time Since Dose is selected as shown above. All three dose day variables are also selected. The time will be displayed in minutes as per above selection.

5. To group the data based on drug days, check the Group by Event Date checkbox from Grouping Option.

6. After choosing the output parameters, hit the Update Summary button that generates a report as shown in the figure below.

There are many reports that can be generated using Analysis Builder based on the data stored in a project. More exploration on the Analysis Builder with different options is recommended.

Project 3 a range of 10000 to 10100

There are various subsections on the search screen, those are self-explanatory. The first section is “Subject” as shown in the following figure. A search in this section can be defined based on:

1. Subject Ids (UIDs or Alternate UIDs)

2. Name (First or Last)

3. Range on date of birth

4. Range on age

5. Sex-based

6. Subject group

Enrollment

The next section is enrollment where a search can be restricted based on projects. One can choose a single project or a list of projects from the drop down menu. Also a sub-group if defined can be specified.

Study

In this part search parameters / variables in a project / study can be defined to refine the search. A search can be restricted based on, study Ids, Alternative study IDs, range of study date, modality (MRI,EEG, etc.), Institution (In case of multiple institutions), equipment, Physician name, Operator name, visit type, and study group

Series

A more specific search based on protocol, MR sequence, image type. MR TR value, series number (if a specific series of images is needed) and series group can be defined.

Output

In this section, the structure of the search output can be defined. The output can be grouped based on study or all the series together. The output can be stored in “.csv” file using the summary tab. The Analysis tab is used to structure the pipeline analysis results.

Other Data Queries

Other than imaging data can also be quried using the similar way as mentioned above for the imaging data above. However the required non-imaging data modality can be selected from the modality dropdown menu in the study section as shown below

ID Mapping

The Ids can be mapped using the "Data" menu from the main menu. One can go to the Id-maper page by clicking on the "ID mapper" link as shown below or by selection the ID mapper sub-menu.

The following page will appear that is used to map various Ids.

A list of Ids to be mapped separated by space, tab, period, semicolon, colon, comma and newline can be typed in the box above. the mapping can be restricted to a certain project by selecting the project name from the dropdown menu. The search can only be restricted to the current instance, undeleted subjects and exact matches by selecting the approprriate selection box shown above.

Export

After searching the required data, it can be exported to various destinations.

For this purpose a section named "Transfer & Export Data" will appear at the end of a search as shown in a fiigure below.

Following are some destinations where the searched data can be exported:

Export to NFS

To export the data to a NFS location, you can select the "Linux NFS Mount" option and type the NFS path where you want to download the data.

Export to Remote FTP Site

To export the data to a remote FTP location, you can select the "Remote FTP Site" option and type the FTP information where you want to download the data.

Export to Remote NiDB Site

To export the data to a remote NiDB site, you can select the "Remote NiDB Site" option and select the NiDB site from a drop down menue where you want to download the data.

Export via Web Download

You can select the data to be downloased to the local http location. you can select "Web http download" option for this purpose as shown below.

Export to NDAR/ RDoCdb/NDA

NiDB has a unique ability to download the data that is required to submit to NDAR/RDoC/NDA. It automatically prepares the data according to the NDAR submission requirnments. Also one can download the data inforamation in terms of .csv that is required to submit NDAR data. The following the the two options to download the data accordigly.

Export status

After starting the transfer by clicking the transfer button at the end of the search, a transfer request will be send to NiDB. The status of a request can be seen via Search-->Export Status page as shown below. The status of 30 most recent serches will be shown by default. All the previoius searches can be seen by clicking on the "Show all" button on the left corner of the screen as shown below.

Public Downloads

This is another option in the "Transfer and Export" section to transfer "searched data" and to make it as public downloadable. There are options to describe briefly about the dataset, setting up a passowrd for secure tranmitability and making the public download updateable to the users having rights on the data. One can select "Required Registration" option to restrict the dowload to NiDB users only. An expiration date for the download can be set to 7, 30 and 90 days. One should select "No Expiration" if the public data should be available for longer than 90 days or for indefinite period.

The "public Download" will be created after pressing the "Transfer" button at the end of search page. The public downloads can be accessed via Data --> Public Download menue. The following is a a page with Public download information:

Request a Dataset

Sometimes you as a user have no idea how the data is stored for a particular project, or you don't have permissions to the project. If you are lucky enough to have a data manager, you can send a request for data to a data manager who can then follow your instructions to find the data and send it to them.

To request a dataset from NiDB-based database, select Data --> Request a Dataset. The following page will appear.

Click Submit New Dataset Request button, and fill the following form to request a dataset from the NiDB-databse.

Analysis Builder

Analysis builder is a report generating tool that can be used to generate various types of reports using the stored data in NiDB. This report generating tool builds on the base of various types of data variables that is being stored in the NiDB. This is different than the search tool where you can search different types of data and download it. In this tool you can search the variables those are generated and stored / imported in the NiDB (Example: You can query the variables generated from a task using MRI / EEG data, but not the actual EEG and MRI data). Analysis builder can be reached via Search --> Analysis Builder or you can go to a specific project front page and select the option (Analysis Builder) on the right from "Project tool and settings" and you will land on the following screen.

Usage

Analysis builder is designed to create reports based on various types of parameters from different types of measures. It has been categorized in the various types of measures like MR, EEG, ET, etc. as shown below.

After selecting the project from the drop down menu "Select Project", click "Use Project" button. Now the project just selected will be the current project for data retrieval.

Directory structure

Files associated with this section are stored in the following directory. subjectID, studyNum, seriesNum are the actual subject ID, study number, and series number. For example /data/S1234ABC/1/1.

/data/<SubjectID>/<StudyNum>/<SeriesNum>

Behavioral data is stored in

/data/<SubjectID>/<StudyNum>/<SeriesNum>/beh

Create a Subject

1. Select the correct instance.

2. On the top menu click Subjects --> Create Subject

3. Fill out the information. First name, Last name, Sex, Date of Birth are required

4. Click Add and confirm on the next screen. The subject is now created

5. On the subject's page, select a project from the Enroll in Project dropdown (you might need to scroll down in the dropdown), and click Enroll.

Updating IDs

1. On the subject's page, click the Edit Subject button on the left.

2. In the IDs section, enter the extra ID(s) in the specific project line. Separate more than one ID with commas, and put a * next to the primary ID. Such as *423, P523, 3543

3. Click Update and confirm at the next screen.

4. If demographic data are stored in a redcap (or other) database and NiDB is storing imaging data, make sure to put each ID in each database. In other words, put the redcap ID into the the NiDB ID field and store the S1234ABC ID in redcap.

Upload EEG and ET data

1. On the subject's page, find the Create New Imaging Studies dropdown. Expand that and find the New empty study dropdown. Select the ET or EEG modality, and click Create. Your study will be created.

2. On the subject's page, click the Study number that was just created, and it will show the study.

3. Fill out the protocol name, the date/time of the series, and any notes, then click Create series.

4. Drag and drop your file(s) onto the Upload button. The status of the upload will be shown below the button.

5. Don't click Refresh or press ctrl+R to reload the page. Instead, click the Study n link at the top of the page.

6. If you need to rename or delete files, click the Manage N file(s) button on the study page.

Upload MRI data through the website (small datasets)

Upload the data

1. On the top menu, click Data. Then click the Import imaging button.

2. Click the New Import button.

3. Choose the files you want to upload. These can indivudual files, or zip files containing the DICOM or par/rec files.

4. Data modality should be Automatically detect.

5. Select the destination project

6. Leave the other matching criteria as the defaults

7. Click Upload.

A new row will be created with your upload. MRI data can contain just about anything, so NiDB needs to read through all the files and see what's there.

Once NiDB has parsed the data you uploaded, you'll need to decide which data to actually import.

1. Click the yellow Choose Data to Import button

2. Details about the import will be displayed. On the bottom will be a list of subjects, studies, and series. You can deselect certain series if you don't want to import them, but likely you'll just want to import all of the series, so click the Archive button.

3. Click on the Back button on the page to go back to the import list.

4. Refresh this page and eventually your import should change to a status of Archived.

Upload MRI data through NiDBUploader (large datasets)

Download the NiDBUploader from github: https://github.com/gbook/nidbuploader/releases

Install it and run the program.

Create a connection

1. Fill in the server: https://yourserver.com, and enter your username/password. Click Add Connection.

2. Click on the connection and click Test Connection. It should say Welcome to NiDB after a little while.

Select the data

1. Select a Data Directory at the top of the program. This should be the parent directory of your data.

2. Change the Modality to MR. Uncheck the Calculate MD5 hash...

3. Click Search. This will slowly populate that list with DICOM/ParRec files that it finds.

4. Once it is done loading files, you can select multiple files and click Remove Selected if you need to.

Set anonymization options

1. Make sure Replace PatientName is checked.

Set the destination

1. Click the ... button for the Instance, which will populate the list of instances. Select your instance. Then select the Project.

2. Click the ... for the Site and Equipment to load the lists. Select the Site and Equipment.

Upload the data

1. Click Upload.

2. It will take a while. Like a long time. Be prepared for that. Depending on the number of files, it could take hours to upload.

3. If any files fail, it will be displayed along with a reason. If you fix the errors, then you can click Resend Failed Objects.

Directory structure

Files associated with this section are stored in the following directory

/data/<SubjectID>

data-dictionary-item

Directory structure

Files associated with this section are stored in the following directory.

/data-dictionary