Cancer Imaging Phenomics Toolkit (CaPTk)  1.6.1
Brain Cancer: Population Atlas

This application facilitates the users to generate population atlases for patients with different tumor subgroups [1] to emphasize their heterogeneity.


  1. Segmentation labels of the tumor sub-regions: Non-enhancing tumor core (Label=1), Enhancing tumor core (Label=4)
  2. Groups: A csv file having patient's label file name e.g. SegmentationLabel.nii.gz (in first column) and group (in second column). (Note that the CSV file should be in ASCII format)
  3. Standard atlas: A standard atlas to map all the patients in a unified space.
  4. The data (segmentation label files) of multiple patients should reside under the same folder, e.g.:
    • Data_of_multiple_patients
      1. Subject_ID1.nii.gz
      2. Subject_ID2.nii.gz
      3. ...
      4. Subject_IDn.nii.gz


  1. Launch the Population Atlases application using the 'Applications -> Population Atlas' menu option.
  2. Specify the Input (e.g., Data_of_multiple_patients) and Output directories, groups and atlas files.
  3. Click on 'Run PopulationAtlas" and the atlases will be displayed in the visualization window.
  4. This application is also available as with a stand-alone CLI for data analysts to build pipelines around, using the following example command:
    PopulationAtlases.exe -i C:/PopulationAtlasesInput -l C:/GroupFile -a C:/AtlasFile -o C:/populationAtlasesOutput


  1. M. Bilello, H. Akbari, X. Da, J.M.Pisapia, S.Mohan, R.L.Wolf, D.M.O'Rourke, M.Martinez-Lage, C.Davatzikos. "Population-based MRI atlases of spatial distribution are specific to patient and tumor characteristics in glioblastoma", Neuroimage Clin. 12:34-40, 2016. DOI:10.1016/j.nicl.2016.03.007