7. DICOM Operations and De-identification

The DICOM operations are available under File > DICOM (command group). These commands include de-identification (anonymization) tools, as well as commands for manipulating DICOM files and folders.

The list of commands changes depending on whether any images are open in FireVoxel. Some commands are always accessible, while others are available only with or without images open.

Note: DICOM > Open selected SERIES is described in the Open section.

7.1. De-identification

Patient privacy rules and research regulations often require that research data be de-identified (anonymized). FireVoxel offers its users broad discretion over de-identification of images. Users are able to customize the de-identification options according to their local privacy regulations, research needs, and processing tasks, which may dictate which information is considered sensitive and how strict the anonymization should be.

Caution!

Users are responsible for complying with the local patient privacy laws when working with images that may contain identifying information.

Default FireVoxel PHI Profile

Fig. 7.1 Default FireVoxelPHIProfile.txt.

The DICOM header fields that contain the information identifying the subject, physician, operator, and imaging center are usually considered Protected Health Information (PHI).

In the US, the Health Insurance Portability and Accountability Act (HIPAA), provides the standard for de-identification of protected health information and lists 18 identifiers that must be treated with special care.

Image processing software packages typically offer de-identification commands, but the list of sensitive DICOM fields (tags) removed by these commands varies by software package (for a comparison of free de-identification tools, see Aryanto 2015 PMID: 26037716).

In FireVoxel, de-identification is performed using commands under File > DICOM:
De-identify DICOM folder (with and without images open) and
De-identify document (only with images open).

FireVoxel allows the user to customize de-identification through the PHI profile, a list of header fields stored in a text file named FireVoxelPHIprofile.txt (Fig. 7.1) in the FireVoxel directory and used by the de-identification commands.

The default FireVoxel PHI profile contains only the most important identifiers listed in order of their field codes (i.e., 0008,0080; 0008,0081; 0008,0090;…).

The user may customize this PHI profile by editing FireVoxelPHIProfile.txt, adding or removing DICOM fields, and then saving these changes. Each field name must be placed in a separate line. The order of the fields does not matter. The new PHI profile takes effect when FireVoxel is started next time. The user should keep a backup copy of the custom PHI profile, because FireVoxelPHIProfile.txt will be overwritten when FireVoxel is reinstalled or updated to a new build. To restore the default PHI profile, the user may overwrite FireVoxelPHIProfile.txt with the list of tags shown in the sidebar.

Note: Retired DICOM tags

The DICOM fields retired from the current standard, but found in older images, are listed in FireVoxelPHIProfile.txt as RETIRED_[tag]. For example, retired tag OtherPatientIDs (0010,1000) is listed as RETIRED_OtherPatientIDs.

For a complete list of DICOM fields and their descriptions, see DICOM Standard Browser.

7.2. DICOM Operations

7.2.1. Show PHI profile

Creates and opens a copy of FireVoxelPHIProfile.txt, named CurrPHIprofile.txt (by default located in Temp directory).

7.2.2. De-identify DICOM folder

Deletes fields listed in FireVoxelPHIProfile.txt from all images in the user-selected selected directory.

Opens browse-for-folder dialog to select a directory containing DICOM images that need to be de-identified.

Once the user selects the directory, a failsafe dialog appears and asks the user to confirm the operation: All DICOM files in [selected directory] will be overwritten. Proceed?

If the user clicks Yes, the files in the selected directory will be replaced with the de-identified files named image_00, image_01, etc. with fields listed in FireVoxelPHIProfile.txt removed.

Once the operation is completed, an information dialog will report the results: [number] out of [total number] of files were de-identified. Time elapsed = [time] sec.

Clicking No cancels the operation.

7.2.3. De-identify document

Available only when images are open in FireVoxel and displayed in a document window.

Removes DICOM fields listed in FireVoxelPHIProfile.txt from the images displayed in the active document window. Opens a dialog showing the list of PHI fields found in the active document (Protected Health Info is present, Fig. 7.2).

The user may choose to De-identify or Cancel. If the user selects De-identify, the PHI fields are deleted only within the active document. The source DICOM images (outside FireVoxel) are NOT de-identified. Select Layer Control > Info to verify that the sensitive tags are no longer present.

De-identify document opens PHI is Present dialog

Fig. 7.2 De-identify document command opens PHI is Present dialog.

7.2.4. Split multiframe DICOM file

Available only when NO images or documents are open in FireVoxel.

Separates a multiframe DICOM image (3D or 4D) into individual frames and writes the resulting image series into a user-selected target directory. The images in the target directory may then be loaded into FireVoxel using File > Open DICOM folder: Single Document.

Opens browse-for-file dialog to select a multiframe DICOM file (.dcm). Once the user selects the file, the command opens a browse-for-folder dialog to choose (or create) a target directory. The command then proceeds to split the original image into individual frames, each slice as a separate DICOM file (.dcm), and saves them in the target directory.

A multiframe image contains a sequential set of image frames, all with the same dimensions and orientation, with a single header. This results in a more compact representation than a regular, single-frame series, in which every image has its own header. Multiframe images may be created, for example, by imaging systems that produce output in the preclinical DICOM format.

Multiframe images may be identified by the following attributes in their headers: (1) Number of Frames (0028,0008), (2) Frame Increment Pointer (0028,0009), and (3) Stereo Pairs Present (0022,0028). Such images may not be supported by some DICOM viewers and cannot be directly opened in FireVoxel without being first split into an image series.

7.2.5. DICOM folder total Pixel Element size

Available only when NO images or documents are open in FireVoxel.

Opens browse-for-folder dialog and returns for the images in the selected folder the sizes (in bytes):
- Total DICOM file size,
- Total DICOM Pixel Element file size.

The total DICOM file size is the sum of the sizes of individual images in the series. The total DICOM pixel element file size is the image size excluding the header. This information can be copied and pasted elsewhere (using Ctrl+C, Ctrl+V).

Note:

Starting with build 369, the pixel element size of zero is returned for uncompressed DICOM files. A non-zero size value is returned for images saved in JPEG Lossless or JPEG-LS formats. See also File > User Interface Options > Compression.

The purpose of this command is to provide an estimate of the relative sizes of the header and image pixel data.

7.2.6. Minimize DICOM headers in Current Document

Available only when images ARE open in FireVoxel and displayed in a document window.

Display fewer DICOM tags in the active document. Removes non-essential tags that are not PHI tags.

7.2.7. DICOM Tree to folders

Copies DICOM images from a user-selected directory, sorts them according to the DICOM Tree structure by Patient, Study, and Series, and pastes copies of these images into automatically created folders named Patient_N, Study_X, Series_Y.

The command opens a dialog panel with boxes for entering/selecting the Source Folder and the Target Folder.

The Source Folder is the directory with the original, unsorted DICOM images. The Target Folder is the location where the sorted images will be placed. After the user specifies the Source and Target folders, a dialog appears: “Include Patient Name as part of the folder name?”

If the user selects Yes, the top directory within the target folder will be named PATIENT_[PatientNameFirst]_[PatientNameLast]_PatientSex_PatientBirthDate.

If the user selects not to include patient’s name, this directory is named PATIENT_1. REVIEW

The next level directory (or directories) inside PATIENT_[…] will be labeled STUDY_[StudyDescription]_[StudyDate] (after DICOM fields).

Still deeper level directories are named SERIES_MN_[SeriesDescription], MN = 00, 01, 02…

Inside each SERIES directory, images are labeled image_00.dcm, image_01.dcm, etc.

7.2.8. Open selected SERIES

Custom image loading option, see Open > DICOM: Open selected SERIES.