Online cross-sectional MS lesion segmentation using FLAIR only images (FIFO Queue)


This is a modified version of nicMSLesions for MS lesion segmentation specifically trained with 46 manually segmented SPMS subjects from the Queen Square Multiple Sclerosis Centre at UCL. This version has been optimised for working with 3D FLAIR MR images. The code is available online at this GitHub repository.

The results will be sent to the following e-mail address:


Select files (Maximum of 10 files with 100 Mb each in .nii or nii.gz formats):
[Select files - FLAIR images]
Your browser doesn't have Flash, Silverlight or HTML5 support.

 By filling in this form I agree to have the provided email address stored in order to use it as email address to send the requested results. I allow use of this email address for contacting me about the project. I understand that NiftyWeb will not disclose this information to any other parties.

Upload files and run the ms lesion segmentation



The queue is empty and MSLESIONS is ready to process your files!
Total files processed so far: 106/106

Publications on this work:

We would appreciate it if the following references would be included in any published work that uses this resource:

  • Ferran Prados, M. Jorge Cardoso, Ninon Burgos, Claudia AM Wheeler-Kingshott, Sebastien Ourselin. NiftyWeb: web based platform for image processing on the cloud. International Society for Magnetic Resonance in Medicine (ISMRM) 24th Scientific Meeting and Exhibition - Singapore 2016
  • http://niftyweb.cs.ucl.ac.uk/

DISCLAIMER: THIS ONLINE TOOL IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.