DICOM Image Management

If you primarily work with images in DICOM format, rather than one of the multi-slice formats such as NIFTI, Jim has the facility to store your DICOM images to a local database, should you wish to do so. This will allow you to:

Store all your DICOM images in one location.
Find out what images you have without running the Image Converter to look through the image headers.
Manage the images, using the Database Manager tool.
Assign images to individual clinical trials or clinical studies.
For longitudinal studies, assign images to different trial time points.
For multi-centre studies, assign images to different centres.
Run database queries to retrieve images with certain features.

There are 3 different tools involved when using a DICOM image database:

The Storage Server tool. Use this to set up the local database, including where to store the database.
The Query Retrieve tool. Use this to query and retrieve images from the local database.
The Database Manager tool. Use this to manage the local database: directly import images to the database; remove images from the database; manage the clinical trials.

Setting up the Storage Server

You can store all images received by the DICOM Storage Server to a database if you set it up to do so. To set it up, you need to:

Enable 'Store to database'.
Set the Database name. This is the name given to the database folder. A folder with this name will be created to contain the image database.
Set the Database directory. This is the top-level folder in which your database will be stored. This folder must already exist.
Set the Database port. This is the TCP/IP port number used to communicate with the database. The usual (and default) port number for database communications is 1527.

When you start the Storage Server with these settings for the first time, the database will be automatically created, and whenever an images is received by the Storage Server, the image details will be saved to the database.

Querying the Database

To query the local database, you need to set up a connection to the local DICOM Storage Server which you started running in the step above. Unless the DICOM Storage Server is running, you will not be able to query the database. In the Query Retrieve tool, on the Node menu, select 'Add node ...'. This will bring up a dialog like the one below, to set up a new node.

Adding a local node to the Query/Retrieve tool

You should enter:

The node name. This is an arbitrary name by which you want to refer to the node.
The node's I/P address. This is the I/P address of the computer on which the Storage Server is running. It may well be the current computer's I/P address. If it is, you can also enter the address 127.0.0.1, which always refers to the current computer.
The port number for connection to the Storage Server. This is the same port number that you set in the Storage Server.
The Application Entity (AE) Title. Again, this is the AE title that you gave to the Storage Server.

You can verify that it is set up correctly by pressing the Button to verify the DICOM connection

button. When all is correct, click the Button to add the DICOM configuration

button to add the node.

You can now select this new node in the Query Retrieve tool, and query the local database as you would any other DICOM server.

Managing the Database

The standalone program DBManager is used to manage the database, which brings up:

The database manager GUI tool

Note that the details of the database configuration being used are shown near the top of the tool. However, this configuration is set up using the Storage Server. The DBManager can be used to:

Query the database directly.
Import images directly to the database. From the Images menu, select "Import images ...", then select the folder that contains the DICOM images you want to import.
Manage clinical trials in the database.
Delete images, undelete images and purge (permanently delete) images from the database.

To query the database, enter the query as you would using the Query Retrieve tool, and click the Button to search the DICOM database

button. If you want to include deleted images in the results returned, the select the Check box to include deleted images in the results returned

check box.

To delete images from the database, with the mouse over either a patient/study or a series node, click the right mouse button and select "Delete":

Delete an image series from the database

A deleted node is shown with a red background. You can undelete an individual node by clicking with the right mouse button and select "Undelete":

Delete an image series from the database

Deleted images are still retained in the database, but do not show up in regular searches using either the Query Retrieve tool or the DBManager (unless the Check box to include deleted images in the results returned

check box is selected).

You can undelete all currently deleted images in the database, by selecting "Undelete all" from the Maintenance menu. You can also permanently remove all deleted images from the database, by selecting "Purge database" from the Maintenance menu. When you do this, you will be asked:

Dialog to confirm purging the database

If you select "Yes", you will then be asked:

Dialog to ask about what you want to do with the images on disk

If you purge the database, only the scan details stored in the database will be deleted permanently: the actual images will not automatically be removed. Select:

Yes, if you want to delete the scan details from the database and also the images themselves.
No, if you want to delete the scan details from the database but keep the images on disk.
Cancel, to cancel the purge operation.

Clinical Trial Management

Setting up a trial

You can use the DICOM database as part of you clinical trials management system. The database can be used to:

Assign Trial sponsors, Trial IDs and Names
Assign particular scans to trial time points
Manage trial sites and assign scans to trial sites
Give individual scans trial-specific names

To get started creating a clinical trial, select "New trial" from the Clinical Trial Menu. This will bring up a dialog to enter the sponsor name:

Dialog to add a trial sponsor

Enter the sponsor name, and click the Button to add a trial

button. This will bring up another dialog for you to enter the Trial Protocol ID number and the Trial Name:

Dialog to set the trial protocol

Next, if this is a longitudinal study, set some clinical trial time points. From the Clinical Trial Menu, select "Manage Trial Time Points". This brings up a dialog for you to select the trial whose time points you want to manage.

Dialog to select a clinical trial

Select the trial from the menu, and click the "Manage time points" button, which brings up:

Dialog to manage clinical trial time-points

For each time point, enter a time point ID and (optionally) a description of the time point. You can reorder the time points into chronological order if necessary by selecting a time-point in the list and clicking the Button to move a time point up the list

and

buttons. Click the Button to finish

button when the list of time points is complete and in chronological order.

Then, you may wish to assign some scanning sites to particular scans in a particular trial so that the scans from particular sites can easily be searched for. From the Clinical Trial Menu, select "Manage Trial Sites". This brings up a dialog for you to select the trial whose sites you want to manage. Select the trial from the menu, and click the "Manage trial sites" button, which brings up:

Dialog to manage clinical trial sites

For each site in the trial, enter a site ID and (optionally) a description of the site.

Finally, you may wish to assign some standard names to particular scans in a particular trial so that they can easily be searched for and recognised. These are the clinical trial series. From the Clinical Trial Menu, select "Manage Trial Series". This brings up a dialog for you to select the trial whose series you want to manage. Select the trial from the menu, and click the "Manage time points" button, which brings up:

Dialog to manage clinical trial series

For each identified series, enter a series ID and (optionally) a description of the series.

Assigning scans to a trial

For any patient in the current list of patients returned by a query, click right on the patient node and select "Assign to clinical trial". This brings up a dialog from which you can select the trial. All image series for this patient/study will be assigned to the trial.

Once a trial has been set for this patient/study, you can then assign the trial time point and trial site (if applicable) using the same pop-up menu:

Pop-up menu to set the clinical trial site and time point

If you click right on one of the individual image series (scans), another pop-up menu will appear from which you can assign the clinical trial series:

Pop-up menu to set the clinical trial series

Once assigned, these same menus can also be used to unassign patients from trials, trial sites, time points and trial series.

If assign clinical trial characteristics to the images in your database in this way, you can then search the database for the characteristics using the Clinical Trial Protocol ID, Clinical Trial Site ID, Trial Time Point ID, or Trial Series ID as query parameters in either the Database Manager or in the Query/Retrieve tool. (If the Query/Retrieve tool, you will also need to select the Show clinical trials search fields checkbox from the Configure menu.

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