8. De-identification and DICOM Operations

The DICOM operations are available under File>DICOM (command group). These commands include de-identification 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.

8.1. De-identification

Patient privacy rules and research regulations often require that research data be de-identified (anonymized). The DICOM header fields that contain 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).

FireVoxel offers its users broad discretion over de-identification. Users are able to customize de-identification options according to their local privacy regulations as well as research needs and circumstances, which may dictate how strict anonymization should be.

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. 8.1) in the FireVoxel directory and used by the de-identification commands.


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

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 to add or remove the fields listed there and 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.

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.

8.2. DICOM Operations

8.2.1. Show PHI profile

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

8.2.2. 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?”

Default FireVoxel PHI Profile

Fig. 8.1 Default FireVoxelPHIProfile.txt.

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 command.

8.2.3. De-identify document (with images)

Available only when images are loaded in FireVoxel. 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. 8.2).

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. 8.2 De-identify document command opens PHI is Present dialog.

8.2.4. Split multiframe DICOM file (without images)

VERIFY Separates a multiframe DICOM file into separate images and writes them in a user-selected directory. Opens browse-for-file dialog to select a multiframe (4D) DICOM file. Once the user selects the file, a browse-for-folder dialog appears to choose the target directory. The command returns a series of DICOM files, each containing a single frame from the original file.

8.2.5. DICOM folder total Pixel Element size (without images)

Opens browse-for-folder dialog and returns (in “image processing” dialog):
1) Total DICOM file size (in bytes)
2) Total DICOM Pixel Element file size. WHY IS PIXEL SIZE ZERO?

This information can be copied (using Ctrl+C keys) and pasted (Ctrl+V) elsewhere.

8.2.6. Minimize DICOM headers in Current Document (with images)

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

8.2.7. 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.