Publications related to STIR
The main publication describing STIR is:
Kris Thielemans, Charalampos Tsoumpas, Sanida Mustafovic, Tobias Beisel, Pablo Aguiar, Nikolaos Dikaios, and Matthew W Jacobson,
STIR: Software for Tomographic Image Reconstruction Release 2,
Physics in Medicine and Biology, 57 (4), 2012 pp.867883.
Please refer to this paper if you use STIR.
If you use STIR for SPECT, please also refer to
BM Fuster, C Falcon, C Tsoumpas, L Livieratos, P Aguiar, A Cot, D Ros, K Thielemans,
Integration of advanced 3D SPECT modeling into the opensource STIR framework,
Medical Physics 40 (9), 092502, 2013.
Below is a handcrafted list of papers that describe STIR.
There is also a corresponding (and more useful)
database on CiteULike. If you use a specific STIR feature described in one of these papers, a reference would be appreciated.
A (probably incomplete) list of references to papers that use STIR is available on this CiteULike page.
There's a Wiki page with instructions on how to add your
own paper to those lists.
Contents

Jacobson M, Levkovitz R, BenTal A, Thielemans K, Spinks T, Belluzzo D, Pagani E, Bettinardi V, Gilardi M C, Zverovich A and Mitra G Enhanced 3D PET OSEM Reconstruction using interupdate Metz filters, Phys. Med. Biol. 45 No.8 (2000) 24172439)
.
This paper describes an alternative regularisation method for EMML using
interupdate filtering (which is somewhat similar to interiteration filtering).
It also describes the subset scheme used by STIR and gives some details on the
parallelisation scheme used during PARAPET (which formed the basis for the current STIR MPI work).

V. Bettinardi, E. Pagani, M.C. Gilardi, S. Alenius, K. Thielemans, M. Teras, and F. Fazio,
Implementation and evaluation of a 3D One Step Late reconstruction algorithm for 3D Positron Emission Tomography studies using Median Root Prior,
Eur. J. Nucl. Med. (2002) Vol 29 No. 1 pp 718).
MRP using STIR.

C. Tsoumpas, F. Turkheimer, K. Thielemans,
Study of direct and indirect parametric estimation methods of linear models in dynamic positron emission tomography,
Med. Phys. Volume 35, Issue 4, (2008) pp. 12991309)

Georgios I. Angelis, Kris Thielemans, Andri C. Tziortzi,
Federico E. Turkheimer and Charalampos Tsoumpas,
Convergence Optimization of Parametric MLEM Reconstruction for Estimation of Patlak Plot Parameters,
Journal Computerized Medical Imaging and Graphics (Feb 2011)
This study reveals how direct iterative reconstruction of kinetic parameters from the
measured (FDOPA) data can be performed optimally (using STIR release 2.1). It explains how to
optimize the speed of the algorithm minimizing bias; and it compares the results with analytic reconstructions.

Polycarpou I; Thielemans K; Manjeshwar R; Aguiar P; Marsden PK; Tsoumpas C
Comparative evaluation of scatter correction in 3D PET using different
scatterlevel approximations,
Annals of Nuclear Medicine (July 2011)
This paper describes how to perform scatter correction using STIR
and it evaluates its accuracy versus SimSET scatter estimation.
Results demonstrate that in many cases scaling the single
scatter distribution is a reasonable approximation to compensate for total
scatter, especially if scaling is based on a global fit.

Kris Thielemans, Charalampos Tsoumpas, Sanida Mustafovic, Tobias Beisel, Pablo Aguiar, Nikolaos Dikaios, and Matthew W Jacobson,
STIR: Software for Tomographic Image Reconstruction Release 2,
Physics in Medicine and Biology, 57 (4), 2012 pp.867883.

Polycarpou I; Tsoumpas C; Marsden PK (Oct 2012) Analysis and comparison of two methods for motion correction in PET imaging. Medical Physics. 39(10): 64746483.

BM Fuster, C Falcon, C Tsoumpas, L Livieratos, P Aguiar, A Cot, D Ros, K Thielemans,
Integration of advanced 3D SPECT modeling into the opensource STIR framework,
Medical Physics 40 (9), 092502, 2013.

Tsoumpas C; Polycarpou I; Thielemans K; Buerger C; King AP; Schaeffter T; Marsden PK (Mar 2013) The effect of regularization in motion compensated PET image reconstruction: A realistic numerical 4D simulation study. Physics in Medicine and Biology, 58(6):17591773.
We have performed two realistic numerical 4D simulation study to compare the two main approaches for PET motioncompensation: motion correction within reconstruction versus postreconstruction (Polycarpou et al, 2012) including medianrootprior regularisation (Tsoumpas, et al 2013) . Both techniques are based on the same iterative reconstruction algorithm in STIR (i.e. OSMAPOSL) approaches are available in the 2.4 release.

Labbé C, Thielemans K, Belluzzo D, Bettinardi V, Gilardi MC, Hague DS, Jacobson MW, Kaiser S, Levkovitz R, Margalit T, Mitra G, Morel C, Spinks T, Valente P, Zaidi H, Zverovich A,
An objectOriented Library for 3D PET Reconstruction using Parallel Computing,
Proceedings of "Bildverarbeitung fuer die Medizin 1999, AlgorithmenSystemeAnwendungen", Informatik aktuell, Springer, Eds. H. Evers, G. Glombitza, T. Lehmann, H.P. Meinzer, pp 268272.

Labbé C, Thielemans K, Zaidi H, Morel C,
An objectoriented library incorporating efficient projection/backprojection operators for volume reconstruction in 3D PET. Proc. of 3D99 Conference, June 1999, Egmond aan Zee, The Netherlands.
PDF
 Thielemans K, Jacobson M W, Belluzzo D,
On various approximations for the projectors in iterative reconstruction algorithms for 3DPET. Proc. of 3D99 Conference, June 1999, Egmond aan Zee, The Netherlands, pp 232235.
PDF,

S. Mustafovic and K.Thielemans,
Additive and Multiplicative versions of the Maximum A Posteriori Algorithm with the Median Root Prior,
proc. IEEE Medical Imaging Conf. 2001.

C. Tsoumpas, P. Aguiar, K. S. Nikita, D. Ros, K. Thielemans,
Evaluation of the Single Scatter Simulation Algorithm Implemented in the STIR Library,
proc. IEEE Medical Imaging Conf. 2004.

K. Dinelle, K. Thielemans, C. Tsoumpas, T. J. Spinks,
An Evaluation of Various Analytic Reconstruction Algorithms and
Implementations for 2D and 3D PET,
in IEEE Medical Imaging Conf. 2004, vol. 7, Oct. 2004, pp. 40434047.

Kris Thielemans, Sanida Mustafovic, Charalampos Tsoumpas,
STIR: Software for Tomographic Image Reconstruction Release 2,
Proc. IEEE Medical Imaging Conference 2006 (San Diego, CA).

T. Beisel, S. Lietsch, K. Thielemans,
A Method for OSEM PET Reconstruction on Parallel Architectures Using STIR,
Proc. Medical Imaging Conf. 2008 (Dresden, Germany).

Berta Marti Fuster, Kjell Erlandsson, Carles Falcon, Charalampos Tsoumpas, Lefteris Livieratos, Domenec Ros, Kris Thielemans,
Evaluation of the novel 3D SPECT Modelling Algorithm in the STIR Reconstruction Framework: Simple vs. full attenuation correction,
proc. IEEE Medical Imaging Conf. 2013 (Seoul, S. Korea).
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