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: pincram-0.2.15.tar.gz (7.3 KiB). (Old version: pincram-0.2.7.tar.gz, 5.5 KiB.) 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.tar (1.1 GiB). We are in the process of preparing a special atlas for labelling the intracranial volume.


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