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DICOM Import

The DICOM Import dialog provides specialized tools for loading medical imaging data in DICOM format. It supports series detection, slice preview, metadata inspection, anonymization, and advanced series refinement for complex acquisitions.

Medical Use Disclaimer

Volvicon is not a regulated medical device. It has not been cleared by the FDA, CE-marked, or approved by other regulatory bodies for clinical diagnosis, treatment planning, or any medical decision-making purpose.

Results from Volvicon should not be used for clinical decisions without validation by qualified healthcare professionals using approved devices.

You are responsible for:

  • Compliance with local privacy regulations (HIPAA, GDPR, etc.)
  • Appropriate handling of protected health information (PHI)
  • Application of anonymization when required
  • Validation of results before any clinical use

Dialog Overview​

The DICOM Import dialog contains the following sections:

SectionPurpose
Directory SelectionBrowse to and load DICOM files from a folder
Series TableView detected series with metadata; select series to import
PreviewScroll through slices of the selected series
Data TabsInspect DICOM tags and file paths for the selected series
OptionsConfigure anonymization, metadata import, and window/level behavior

Workflow: Basic DICOM Import​

  1. Open the DICOM Import dialog via File → New → DICOM Images or File → Import → DICOM Images
  2. Click Browse to select a directory containing DICOM files
  3. Click Load to scan the directory (and subdirectories) for DICOM series
  4. Review the detected series in the Series table
  5. Select the series to import by clicking its row
  6. Preview slices using the slider to verify correct data
  7. Configure options:
    • Anonymize DICOM tags to remove identifying information
    • Do not import DICOM tags to import pixel data without metadata
    • Use DICOM window and level to apply display values from the selected series
  8. Use Subrefine series if a mixed acquisition needs additional separation criteria before import
  9. Click Open to import the selected series

Coordinate System After Import​

Volvicon imports DICOM series into its internal volume orientation for viewing and processing. The voxel values, spacing, and origin are preserved from the series unless you explicitly enable mismatch resampling in Preferences. The original DICOM orientation is not retained as a separate direction matrix on the imported volume.

DICOM uses the LPS (Left-Posterior-Superior) patient coordinate system, where the three image axes point toward the patient's left, posterior, and superior directions. RAS (Right-Anterior-Superior) is the convention used by many neuroimaging tools such as 3D Slicer, where the first two axes are reversed relative to LPS.

Basis+X+Y+Z
LPSLeftPosteriorSuperior
RASRightAnteriorSuperior
warning

Changing the View orientation preset changes axis labels and slice naming in the user interface, but it does not modify the underlying voxel data.

AI Inference​

TotalSegmentator and nnU-Net require RAS orientation. When Make image orientation compatible is enabled (the default), Volvicon provides the orientation information these frameworks need without changing the image data.

The Output options panel in the AI Segmentation widget contains a Make image orientation compatible checkbox (default: enabled) for TotalSegmentator and nnU-Net. Leave it enabled for standard DICOM-imported volumes. Disable it if you have already manually converted the volume to RAS before running — for example by flipping both X and Y axes about the origin — otherwise the orientation correction would be applied twice and produce incorrect results.

MONAI and Cellpose-SAM use the volume's current orientation. Volvicon does not add orientation information for these frameworks.

Display Alignment with Other Applications​

If you need the displayed Volvicon views to match a RAS-based application such as 3D Slicer, flip the X and Y axes about origin via Image → Flip:

  1. Open Image → Flip.
  2. Flip X with Flip Reference set to About origin.
  3. Flip Y with Flip Reference set to About origin.
  4. Verify left/right and anterior/posterior anatomy in the slice views.
note

Use About origin for this conversion. About center mirrors the object around its own center and produces a different result.

After this flip the volume is in RAS orientation. If you then run TotalSegmentator or nnU-Net, uncheck Make image orientation compatible in the Output options panel — the volume is already in RAS so the header correction is not needed. Verify that the anatomy appears correct in the slice views before proceeding.

Volumes imported from other formats or exported by other applications may already be RAS or may use another basis. If the problem is an exchanged axis order rather than an inverted axis direction, use Swap Axes instead of a flip.

Series Detection and Selection​

Series Table Columns​

The series table displays key metadata for each detected series:

ColumnDescription
Series #DICOM Series Number
ModalityImaging modality (CT, MR, etc.)
Study DateDate the study was acquired
Series DateDate the series was acquired
Patient IDPatient identifier (anonymized if option enabled)
Study Instance UIDUnique identifier for the study
FilesNumber of DICOM files in the series

Multi-Series Selection for 4D Data​

When multiple series share compatible geometry (same dimensions, spacing, and orientation), you can multi-select them for 4D import:

  1. Hold Ctrl and click to select multiple series
  2. Each selected series becomes a time frame in a single 4D volume
  3. The series must have matching geometry for valid 4D assembly
  4. The series that remains selected when you click Open supplies the initial frame and display settings for the imported volume
note

Multi-selection is only enabled for series with compatible geometry. If series cannot be combined, multi-selection is disabled.

4D Import Scope and Current Limitations​

When a compatible multi-series selection is imported, Volvicon stores the selected series as frames in a single volume object. This enables playback in Cine Loop.

Current 4D Support Scope

4D support is currently limited to the imported volume object.

  • Cine loop playback is available for volume objects only
  • Masks, surfaces, and volume meshes do not store synchronized 4D frame sets
  • Most tools operate on the current active 3D frame, not on the entire time sequence

Workflow: Import a 4D DICOM Series for Cine Loop​

  1. Load the DICOM directory and review the detected series
  2. Hold Ctrl and select the compatible series that belong to the time sequence
  3. Verify slice preview and metadata before import
  4. Click Open to create a single volume object with multiple stored frames
  5. Open Cine Loop from the View tab to review the imported sequence
tip

If you plan to use Cine Loop after import, keep the 4D sequence unchanged until review is complete. Geometry-changing operations can invalidate the stored frames.

Series Refinement​

Complex DICOM directories may contain mixed acquisitions that share the same Series Instance UID but represent different phases, orientations, or acquisition parameters. Use Subrefine series to add filtering criteria that separate these into distinct series.

Workflow: Refining Series​

  1. Click Subrefine series... below the Series table
  2. In the Refine dialog, select additional DICOM tags to use as separation criteria:
CategoryAvailable Tags
DescriptiveStudy Description, Series Description, Patient's Name, Protocol Name
AcquisitionAcquisition Number, Image Orientation (Patient)
TemporalTrigger Time, Echo Time, Repetition Time, Acquisition Time, Series Time, Content Time, Delta Start Time
SequenceFlip Angle
  1. Click OK to re-analyze the directory with the additional criteria
  2. The Series table updates to show refined series separation
tip

Use series refinement when:

  • A folder contains multiple scan phases (arterial, venous, delayed)
  • Different orientations are mixed in the same series
  • Time-resolved acquisitions need separation by acquisition time

Slice Preview​

The preview panel displays slices from the currently selected series:

  • Slider: Scroll through slices from first to last
  • Spin Box: Enter a specific slice number for direct navigation

The preview uses DICOM window/level values when available, showing the data as it would appear in a DICOM viewer.

Data Inspection​

Two tabs provide detailed information about the selected series:

DICOM Tags Tab​

Displays the DICOM metadata (tags) from the selected series. Common tags include:

TagDescription
Patient NamePatient identifier
Study DescriptionDescription of the imaging study
Series DescriptionDescription of the series
ModalityCT, MR, US, etc.
Pixel SpacingIn-plane pixel dimensions
Slice ThicknessDistance between slices
Window Center/WidthDefault display window/level

Files Tab​

Lists all DICOM files that comprise the selected series, including file paths. This helps verify that the correct files are included and identifies the source locations.

Import Options​

Anonymize DICOM Tags​

Default: Enabled

When enabled, Volvicon removes identifying information from the imported DICOM metadata according to the application-level confidentiality profile. This includes patient name, ID, birth date, and other identifying tags.

warning

Anonymization removes identifiers from DICOM tags stored in the project file. It does not:

  • Remove burned-in annotations in pixel data
  • Affect the original DICOM files on disk
  • Guarantee complete de-identification for all use cases

For regulated environments, validate that your anonymization requirements are fully met.

Disabling anonymization displays a privacy warning. Only disable this option when you have explicit authorization to retain identifiable information.

Do Not Import DICOM Tags​

Default: Disabled

When enabled, only pixel data is imported—no DICOM metadata is stored in the project. This option:

  • Completely omits metadata storage
  • Disables the anonymization option (nothing to anonymize)
  • May affect features that rely on DICOM metadata

Use this option for maximum metadata stripping when no DICOM information should be retained.

Use DICOM Window and Level​

Default: Enabled

When enabled, Volvicon applies the window center and width values from the DICOM metadata to the preview and imported volume. This displays the data using the acquisition device's recommended viewing parameters.

When disabled (or if DICOM window/level tags are absent), Volvicon computes optimal window/level values from the actual image intensities.

Best Practices​

Before Import​

  1. Organize DICOM files: Keep series in dedicated folders for cleaner detection
  2. Review metadata: Check for mixed acquisitions that may need refinement
  3. Verify orientation: Preview slices to confirm expected anatomy

Privacy Considerations​

  1. Enable anonymization unless you have specific authorization to retain identifiers
  2. Review the project before sharing to ensure no identifying information persists
  3. Follow institutional policies for handling medical imaging data

Multi-Modality Studies​

When importing multiple imaging modalities into a single project:

  1. Import each modality separately using the DICOM Import dialog
  2. Verify alignment in orthogonal views
  3. Use registration tools if spatial alignment is required

Working with Imported 4D Volumes​

  1. Use Cine Loop to review the time sequence before running crop, resample, or similar geometry-changing operations
  2. Pause on the frame of interest before using tools that operate on the current active volume
  3. Re-import the 4D dataset if you need cine playback after a geometry-changing edit
warning

If the active volume geometry changes after 4D import, Volvicon clears the stored frames and keeps the current active volume image. This prevents playback of frames that no longer match the modified geometry.

Troubleshooting​

No Series Detected​

  • Verify the directory contains valid DICOM files
  • Check that files have .dcm extension or valid DICOM headers
  • Try a parent directory if files are in subdirectories

Series Appear Mixed or Incorrect​

  • Use Subrefine series to add separation criteria
  • Check for multiple acquisitions in the same folder
  • Verify that DICOM files haven't been renamed or modified

Preview Shows Incorrect Orientation​

  • DICOM orientation is determined by Image Orientation (Patient) tags
  • DICOM image data is not modified during import; Make image orientation compatible provides the orientation information required by TotalSegmentator and nnU-Net
  • To convert the displayed volume to RAS (e.g. to match a 3D Slicer layout), use Flip: X about origin, then Y about origin; after this flip the volume is already in RAS, so uncheck Make image orientation compatible before running inference
  • Use Swap Axes only if the axes are permuted rather than inverted
  • Changing the View orientation preset does not change the stored voxel orientation

Import Fails​

  • Check available system memory for large series
  • Verify read permissions for the DICOM files
  • Check for corrupted DICOM files in the series

Imported 4D Frames Are No Longer Available​

  • Check whether the volume was cropped, resampled, padded, or otherwise modified after import
  • Review the status bar for the frame-cleared notification
  • Re-import the 4D series if you need Cine Loop playback again