Image data used in this challenge were acquired from five different scanners from three different vendors in three different hospital in the Netherlands and Singapore. For each subject, a 3D T1-weighted image and a 2D multi-slice FLAIR image are provided. The manual reference standard is defined on the FLAIR image.


UMC Utrecht3 T Philips Achieva2030
NUHS Singapore3 T Siemens TrioTim2030
VU Amsterdam3 T GE Signa HDxt2030
3 T Philips Ingenuity010
1.5 T GE Signa HDxt010

For each subject, the following files are provided:

/orig/3DT1.nii.gzThe original 3D T1 image, with the face removed
/orig/3DT1_mask.nii.gzBinary mask used to remove the face.
/orig/FLAIR.nii.gzThe original FLAIR image. This image is used to manually delineate the WMH and participants should provide the results in this image space.
/orig/reg_3DT1_to_FLAIR.txtTransformation parameters used to align the 3D T1 image with the FLAIR image. Participants can use this to do the transformation themselves, in case they use the 3D T1 for processing. Results will be evaluated in the FLAIR space. Call: transformix -in IMAGE.EXT -out /output -tp /orig/reg_3DT1_to_T2_FLAIR.txt
/orig/T1.nii.gzThe 3D T1 image aligned with the FLAIR image.
/pre/3DT1.nii.gzBias field corrected 3D T1 image.
/pre/FLAIR.nii.gzBias field corrected FLAIR image.
/pre/T1.nii.gzBias field corrected T1 image, aligned with FLAIR.
/wmh.nii.gzManual reference standard, only available for training data.

Example images

orig/3DT1orig/3DT1 maskorig/FLAIRorig/T1
Top row shows all images present in the folder orig. Bottom row shows the pre-processed images and the manual WMH segmentation.

Folder: orig

This folder contains the original images, anonimized and having the face removed. The mask used to remove the face from the 3D T1 images is provided. The 3D T1 image has been aligned with the FLAIR image using elastix 4.8 with the following parameter file: Elastix parameter file for the WMH Segmentation Challenge.

Folder: pre

All images were pre-processed with SPM12 r6685 to correct bias field inhomogeneities.

Manual reference standard

This file is only provided for the training data. It contains the following three labels:

  1. Background
  2. White matter hyperintensities
  3. Other pathology

The objective of this challenge is to automatically segment WMH. Because we do not require methods to identify all other types of pathology, we provide a rough mask for them that will be ignored during evaluation.

Additional data

Participants are allowed to use additional data to train their method. This must be mentioned in the description that is submitted with the method. We encourage participants to use open data or make the additional data open access.


Participants who have registered their team and signed the confidentiality agreement are eligible to download the data.