User Manual

This section is for regular users: RAs, analysts, etc

Common Tasks

Registering a new subject

Go to the Subjects tab, click New Subject. Enter as much information as you can, click Add.

Enrolling a subject in a project

On an subject’s individual page, select a project from the Enroll subject is project drop down list, click Enroll. The new enrollment will appear, with the current date as the start date, and Jan 1, 3000 as the end date.

Creating a new study (MR)

On the MRI scanner console, enter the UID (S1234ABC) as the Patient ID. If the DICOM receiver is setup on NIDB, the entire imaging study including all series and meta-data will be automatically entered into NIDB. The series should appear within 2 minutes after a series completes and the DICOM images are sent to NIDB. Advanced: Place uniquely named DICOM files (without directories) in the /nidb/dicomincoming directory. If the parsedicom module is enabled, the DICOM files will be automatically parsed and stored in the database.

Creating a new study (all other modalities)

On an subject’s individual page, click Create new study within the project in which you want to create the imaging study. It will create an imaging study with a blank modality, and you will need to edit the study information to change the modality.

Adding family relations

On an subject’s individual page, select a relation from the drop down list and enter the UID of the other family member. Click Add relation. You probably want to leave the Make symmetric box checked so that an equivalent relation will appear in the other family member’s information.

Adding series to studies (non-MR modalities)

Enter the Series #, Protocol, Date, Notes and click Create. You can upload data by dragging and dropping onto the Upload a file box, or by clicking the Upload a file box. You can edit the Protocol, Date, and Notes in place by clicking the light yellow boxes, typing, and hitting <enter>, or you can click the series # and edit the series. You can manage the files associated with each series by clicking on the # of files.

Quick subject search

Click the Subject tab. Enter search criteria, such as Name, UID, Alt UIDs, Gender, DOB and click Search. You may also search for deleted subjects by unchecking the Active? box. Click the UID to view the subject details and studies.

Searching & data retrieval

Click the Search tab. Enter any criteria. Click the Toggle advanced search tab on the left to view more critera. Select the type of results you want, either the ability to download the data or just view it on screen or in a spreadsheet. There is a 35,000 series limit when retrieving search results.
If you want to download data, a list of series will appear with checkboxes on the left. Rows in red indicate that another user has flagged the data as bad. Rows in gray indicate a user has flagged the data as not being actual data, such as a test scan on a pineapple.
Select the series you want to download. At the bottom of the page, you can either add those series/studies/subjects to a group, or download the data. To add to a group, select the group from the drop down list and click Add. To download data, select the destination, data format, and directory format options, and click Download. Information on how to get your data or where it is located appear on the next screen depending on the download method you selected.

Uploading behavioral data (MR)

On a subject’s study page, locate the series you want to upload the behavioral data into. Either drag and drop the files onto the Upload a file box, or by clicking the Upload a file box. Because of browser issues, you will most likely see a message saying ‘Upload failed…” however it did not fail, and if you refresh the page, you will see a number on the rightmost column. Clicking on that number will allow you manage the behavioral data associated with each series.

Other neat stuff to do, by page


View the most recent studies, collected in the past 72 hours. Click NIDB statistics to view information about the content of the database, including motion/age correlation for MR and numbers of imaging studies per month.


Mouseover the page  and camcorder  icons next to the protocol name. This will display a static image of the middle slice of a volume and a cine-movie of the entire volume respectively. Clicking the protocol name will display detailed scan parameters.
Clicking the QA icon  will show motion correction parameters, an FFT of the middle slice, and radial average of the 2D FFT.
The X Y Z columns show quick motion correction information. The top number is the total displacement (for example, -0.5mm to +1.0mm for a total of 1.5mm). The bottom number is the absolute value of the maximum displacement (for example, -2.4mm to 1.3mm, for a maximum displacement of 2.4). These numbers are color coded green to red, with green being 0 and red being the voxel dimension.
Clicking the Ratings icon  will show other user’s opinions of the data and allow you to add your own ratings.
Mouseover the SNR to see a comparison of the current SNR value with all other SNR values for the same protocol name. This isn’t actually useful because it turns out that SNR is not comparable between subjects.

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