This docker container contains a pipeline to preprocess your medical imaging data (MRI, CT, PET, etc.) in anticipation of machine learning or other quantitative analysis. It includes conversion from DICOM to Nifti, skull-stripping, N4 Bias correction, registration, resampling, and label subsetting. It currently uses the software packages 3DSlicer, ANTs, Freesurfer, and FSL.
See documentation at: https://github.com/QTIM-Lab/qtim_PreProcessor