Brain extraction using label propagation and group agreement.
Pincram takes as input
a target image -- T1-weighted 3D magnetic resonance (MR) volume of the human brain in NIfTI format
an atlas database consisting of reference MR images and corresponding binary segmentations (total brain volume masks and intracranial volume masks).
a total brain volume mask (parenchyma plus internal cerebrospinal fluid)
an intracranial volume mask that fully contains the former
a probabilistic segmentation of the total brain
corresponding to the target image.
Pincram works with GNU parallel or PBS to parallelize the atlas-target registrations.
IRTK (https://github.com/BioMedIA/IRTK; a port to MIRTK is in development)
Add pincram directory to PATH. Copy common-template to common and adapt to system. Call
pincram.sh for usage.