Harmonised segmentation of neonatal brain MRI

Author: Irina Grigorescu | irina[dot]grigorescu[at]kcl[dot]ac[dot]uk

This is the companion code for the following publications:

• Grigorescu, I. et al. (2021). Harmonized Segmentation of Neonatal Brain MRI. Frontiers in Neuroscience
  • doi.org/10.3389/fnins.2021.662005

Example train/validation/test file (one subject / line, see example_csv_files folder)

t2w,lab,ga,as,gender
subj1_T2w_brain.nii.gz,subj1_lab_tissue.nii.gz,41.0,41.14,Male
subj2_T2w_brain.nii.gz,subj2_lab_tissue.nii.gz,38.0,39.14,Female

Also, bare in mind that the code currently expects the suffix _T2w_brain.nii.gz for the images, and the suffix _lab_tissue.nii.gz for the segmentation maps. It also expects _lab_all.nii.gz for the cortical parcellation network.