Open DICOM Data

The DICOM browser provides convenient access to DICOM files in the DICOM server or any other specified repository. Reconstructions can be started from the DICOM browser and files may also be exported.

Getting There

Three different methods exist for reaching the DICOM browser.

The first method is to use the DICOM Database thumbnail in the Main Window.

The second method is to go to "Open DICOM data..." under the File menu.

The third method is to use the keyboard shortcut "Ctrl+D". For more on keyboard shortcuts in VQ, please see Keyboard Shortcuts.

Function

The DICOM browser's main window is split into four regions -- Repository, Filter, Data, and Study Browser.

Repository

The repository displays the DICOM browser or local folder from which DICOM files are currently being displayed in the Study Browser. See DICOM Configuration for more information on configuring your DICOM browser, including the use of projects in an iPACS repository.

There is a projects filter within the repository that allows the user to reduce the projects list in order to more easily search for a desired project. There are three ways to filter the project list as described in the following table

Filter Option Description Example
word Reduces project list to all projects that contain the given word in their path. Type 'exampledata' in the projects filter to reduce the projects list to all projects with the word 'exampledata' in their path.
!word Reduces project list to all projects that do not contain the given word in their path. Type '!exampledata' in the projects filter to reduce the projects list to all projects that do not contain 'exampledata' in their path.
&regexp Reduces project list to all projects that match the given regular expression. An example of a commonly used regular expression** is the choice operator, |, which matches either the expression before or the expression after the operator. For example, if the user types '&exampledata|test' in the projects filter, the projects list will reduce to all projects that have the word 'exampledata' and all projects with the word 'test' in their path.

Press enter on keyboard to apply the filter. The filtered number of projects over the total number of projects is displayed. For example, the image below displays 2 out of 198 projects with the word 'exampledata' in their path.

**For more examples of regular expressions supported by the projects filter, click here.

Filter

As a DICOM database grows, the Filter tool becomes useful for sifting through studies to find just the right one. Options for filtering** include Patient's Name, Patient ID, Study Description, and Study Date. After entering values in these available fields, simply hit the refresh filter settings button to refresh the Study Browser. Want to view all of the data again? Simply hit the clear filter button to empty the fields and hit again to refresh the Study Browser.

**Note that filtering uses a Unix-like naming structure. Therefore, if you want to find all studies that begin with Mouse, enter Mouse* in the filter for Patient's Name. In addition, if you wanted to find any study containing I123, enter *I123* in the filter for Patient's Name.

Also available in the filter options is the '+' function, used to expand or collapse the entries currently displayed in the DICOM browser. The first click will expand all data at the patient/study level; the second click will then expand at the series level; the third click will collapse the series level; the fourth click will collapse patients/studies.

Before expansion:

After one click of the "X button":

After the second click of the "X" button:

Expanding large numbers of datasets can take several minutes.

Data

The Data section provides several functions for manipulating data, including sorting, finding, and opening.

Show data type: This pull-down menu can limit the data displayed in the Study Browser to a single modality (i.e., CT) or data type (i.e., reconstructions).
Open This button is used to open the data highlighted in the Study Browser. If a single data file is highlighted, it will be opened as the Reference image. If an entire Study is highlighted, the Open button recognizes which data file is the CT and sets it as the Reference. Use of the Open button unloads data currently in VQ and replaces it with the highlighted data. More information on the relationship between the Study Browser and the Open button can be found in the Study Browser documentation.
Append This button is used to append the data highlighted in the Study Browser to the data sets already loaded into VivoQuant. For example, if two data sets are selected in the Data Browser and three data sets are already loaded into VQ, then appending the two highlighted data sets will cause them to appear as data sets 4 and 5 in the Data Manager. Use the Open button to unload data currently loaded in VQ and replace it with the highlighted data.
Find Enables a search of the Study Browser by looking for user-defined text in one of the available columns (Patient's Name, Study Date, Study Description, or patient ID).
Import Allows DICOM data from a local folder to be imported into another local folder, DICOM repository, or iPACS repository.
Export Allows DICOM data to be copied to a local folder.
Apply default shift If checked, a pre-defined shift will be applied to reconstructed SPECT data when it is opened. See Reorientation for more details on setting default shift values.
Auto-start reconstruction If checked, CT and NM reconstructions will begin automatically when the Open button is applied to projection data in the Study Browser.
Force planar By default, data with voxel widths greater in the z-dimension than in the x and y dimensions will be interpolated to have isotropic voxels when the Open button is applied. To prevent interpolation from being performed on data with non-isotropic voxels, check 'Force planar.'

Data Formats

DICOM data with *.dcm, *.dc3 or *.dicom extensions are supported in the Data Browser by default. To edit this setting and to configure loading in extension-less DICOM data from the DICOM browser navigate to the DICOM Settings page.

Study Browser

The Study Browser displays the DICOM data found in the selected Repository. The Filter, Show Data Type, and Find options can be used to limit the data displayed in the Study Browser. In all cases, the data is opened with either the Open button or the Append button. The Open button will unload data currently open in VQ and load the highlighted data as Reference, Input 1, Input 2, etc. The Append button will leave the currently loaded data unchanged and append the highlighted data. This appended data may be accessed via the Data Manager.

At the top level, multiple files may be opened into the Main Window simultaneously. The DICOM browser recognizes the files in the study and opens them accordingly, setting the CT image as the Reference. If extra data is found, the DICOM browser provides the message, "Ignoring extra data sets."

At the next level, single data sets from a study may be selected for viewing.

This nested structure continues, depending on the format in which the data is saved. For example, for CT data saved in Single Frame format, single slices may be selected for viewing.

"Ctrl-click" and "Shift-click" options are also implemented to simplify data selection. This feature is useful both for selecting subsets of studies to load into the Main Window and also for selecting large groups of studies to Export.

Right-Click function

The right-click function of the DICOM browser is used as a shortcut for opening/exporting CT or NM data and sending it to a batch job (HiSPECT or BatchCT for SPECT and CT data, respectively), reconstruction or DICOM dump. Finally, when working in a local repository (i.e., a local folder as opposed to DICOM or iPACS servers), the right-click option may be used to delete data.

To use this function, highlight either the CT or NM data and right-click. A box with a number of functions is then displayed. The options vary depending on the type of projection data selected.

Within DICOM or iPACS Server

Right-click on the Helical CT or Helical SPECT scan of interest

There are various options depending on the data type available with this tool.

Option Description
Open data Opens the selected data set in VQ and loads it as the reference (see Open Reference).
Export to... Allows DICOM data to be copied to a local folder or to another DICOM or PACS repository.
Open in... Allows DICOM data to be opened in an external Application.
Dump Header Sends the file to the DICOM dump tool, which displays the information contained in the DICOM headers.

Within a Local Repository

When working in a local repository (i.e., a data folder as opposed to a DICOM or iPACS server), the right-click button may also be used to delete data.