Extracting brains from MR head images with PINCRAM

What it is

PINCRAM is a method for masking cranial MR images based on multiple atlases. It is loosely based on MAPER (Heckemann et al., Neuroimage 2010).


Please download pincram here: github.com/soundray/pincram. Pincram requires GNU Bash version 3 or higher. Tested under Debian 8, Ubuntu 14.04, and RedHat Enterprise Linux Server release 6.7. Likely to work under Mac OS X. Dependencies: IRTK and Nifty Seg 0.9.4.


You will also need a suitable source data set. For brain labelling we recommend ixi-pincram-atlas-n100-verified-may2018.tar (1.5 GiB). This atlas database has masks for the total brain volume (includes internal and most sulcal CSF) and for the intracranial volume (as defined by Klasson et al., BMC Medical Imaging 2015).


If you use pincram, please cite the following paper:

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. doi: 10.1371/journal.pone.0129211. eCollection 2015.

Data sets used in the paper

Various atlas sets are used in the paper:


The Hammers Atlas is a database of 30 MRI brain atlases of young healthy adults, available for download from www.brain-development.org (Resources - Atlases - Adult). The segmentations into 83 regions have been carefully prepared using a detailed, validated protocol which is described in the following two papers:

Hammers A, Allom R, Koepp MJ, Free S., Myers R, Lemieux L, Mitchell TN, Brooks DJ, Duncan JS, Aug. 2003. Three-dimensional maximum probability atlas of the human brain, with particular reference to the temporal lobe. Hum. Brain Mapp. 19 (4), 224-247. http://dx.doi.org/10.1002/hbm.10123
Gousias IS, Rueckert D, Heckemann RA, et al., 2008, Automatic segmentation of brain MRIs of 2-year-olds into 83 regions of interest, Neuroimage, Vol:40, ISSN:1053-8119, Pages:672-684. http://dx.doi.org/10.1016/j.neuroimage.2007.11.034


IXI is a database of 575 adult volunteers, available for download from www.brain-development.org (Resources - Datasets).


The LONI Probabilistic Brain Atlas (LPBA40) is a set of atlases prepared from 40 adult human volunteers.


This is the atlas prepared for the MICCAI 2012 Grand Challenge and Workshop on Multi-Atlas Labeling from a subset of 30 adult volunteers selected from the Open Access Series of Imaging Studies (OASIS).

Rolf Heckemann
Email: rolf dot heckemann at medtechwest dot se