add calculation of total and regional brain volumes

[jfpva]

using bounti label volumes

follow calculations in Cromb et al 2023 (doi:10.1002/jmri.29078)

• cortical gray matter (cGM)
• white matter (WM)
• deep gray matter (dGM) (thalamus + lentiform nucleus)
• cerebellum (cerebellar hemispheres + cerebellar vermis)
• total cerebrospinal fluid (CSF) (extra-axial CSF + lateral ventricles + cavum septum pellucidum + third fourth ventricles)
• total brain volume (cGM + WM + dGM, cerebellum, brainstem)

also include volumes:

• each label region
• of 9 structures (combined right and left and associated ROIs) from Uus et al 2023 (doi:10.7554/eLife.88818.1)
  • external CSF (labels 1+2)
  • lateral ventricles (7+8)
  • cavum (9)
  • brainstem (10)
  • 3rd & 4th ventricles (18+19)

output in format that can be easily aggregated across cases for further analysis

[jfpva]

original issue updated to include all volumes based on Uus2023