pincram

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).

It produces

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 xargs or PBS to parallelize the atlas-target registrations.

Dependencies

IRTK (https://github.com/BioMedIA/IRTK; a port to MIRTK is in development)
NiftySeg (http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg).

See also

http://soundray.org/pincram

Instructions

Add pincram directory to PATH. Review run-pincram script for sample invocation. Call pincram.sh for usage.

If you use this software for your research

Please cite: Heckemann RA, Ledig C, Gray KR, Aljabar P, Rueckert D, Hajnal JV, Hammers A. Brain Extraction Using Label Propagation and Group Agreement: Pincram. PLOS ONE. 2015 Jul 10;10(7):e0129211.