GUI preprocessing

Use the Preprocessing tab to convert DICOM data to NIfTI or resample images and masks to a target voxel spacing. The output can then be used for filtering or feature extraction.

Preprocessing tab in the GUI.

Main controls

The numbers below match the annotated screenshot.

(1) Preprocessing tab

Use the top tab bar to navigate between the main parts of the application. This page describes the controls shown when Preprocessing is active.

(2) Input Directory

Select the dataset directory that contains one subfolder per case. For the expected folder layout, see Expected data structure.

(3) Threads

Choose how many case folders to process in parallel. More threads can reduce runtime but use more memory.

(4) Imaging Modality

Select the modality of the input image series or image file set. All cases processed in one run should belong to the same modality.

(5) Start Folder and Stop Folder

Limit processing to a numeric folder range. This only works when the case folders have integer names.

(6) List of Folders

Process an explicit comma-separated set of folders such as 1, 5, 10 or mixed names such as patient_A, patient_B. If neither (5) nor (6) is set, Z-Rad processes every subfolder in the selected input directory.

(7) Output Directory

Choose where to save processed images and masks. Z-Rad creates the directory if needed.

(8) Data Type

Choose whether the input dataset is DICOM or NIfTI. This selection controls which additional preprocessing fields become visible.

(9) Resample Resolution

Sets the target voxel spacing in millimetres.

(10) Mask Union

Combines all selected masks into a single union mask in addition to the individually saved masks.

(11) Image Interpolation

Select the interpolation method used for the image volume. The GUI exposes nearest-neighbour, linear, B-spline, and Gaussian interpolation.

(12) Resample Dimension

Controls whether resampling is performed slice-wise in 2D or volumetrically in 3D.

(13) Mask Interpolation

Select the interpolation method used for masks. When a method other than nearest-neighbour is selected, Z-Rad shows an additional threshold field that converts interpolated values back into a binary mask.

(14) RUN

Starts preprocessing with the currently selected parameters.

DICOM input

Additional options shown when the input data type is DICOM.

For DICOM workflows, the Data Type selection (8) exposes the following controls:

(8.1) Structures

Enter the ROI names from RTSTRUCT files or SegmentLabel values from DICOM SEG files to process.

(8.2) All structures

Process every non-empty structure available in the RTSTRUCT or SEG file.

(8.3) Convert to NIfTI without resampling

Export the DICOM image and selected structures as NIfTI files without changing voxel spacing.

NIfTI input

Additional options shown when the input data type is NIfTI.

For NIfTI workflows, the Data Type selection (8) exposes:

(8.4) NIfTI Masks

Enter one or more mask filenames without file extensions.

(8.5) NIfTI Image

Enter the image filename without file extension.

Missing masks or structures are skipped rather than terminating the run.

Outputs

Z-Rad creates one subfolder per case in the output directory. Each contains image.nii.gz and the processed masks named after their structures, such as GTV-1.nii.gz. Use this directory as input for the next processing tab, with image as the NIfTI image name. See GUI quickstart for the complete workflow.

Resampling and saved settings

See Resampling guidelines for help choosing the target spacing, dimension, image and mask interpolation, and mask threshold.

• 2D resampling preserves the original slice spacing in the third axis.

• CT images are rounded and stored as signed 16-bit integers after resampling.

• MR and PET images remain floating-point volumes.

• Input configurations can be saved from the GUI and later reloaded for reproducible reruns (File -> Save/Load Input or Ctrl+S/Ctrl+O).

For configuration examples, see Preprocessing in GUI.