Journal Articles 

I. Aganj and B. Fischl, “Multimodal image registration through simultaneous segmentation,” IEEE Signal Processing Letters, vol. 24, no. 11, pp. 1661–1665, 2017.  
H. Wang, C. Magnain, R. Wang, J. Dubb, A. Varjabedian, L. S. Tirrell, A. Stevens, J. C. Augustinack, E. Konukoglu, I. Aganj, M. P. Frosch, J. D. Schmahmann, B. Fischl, and D. A. Boas, “asPSOCT: volumetric microscopic imaging of human brain architecture and connectivity,” NeuroImage, in press, 2017.  
T. Tong, I. Aganj, T. Ge, J. R. Polimeni, and B. Fischl, “Functional density and edge maps: characterizing functional architecture in individuals and improving crosssubject registration,” NeuroImage, vol. 158, pp. 346–355, 2017.  
I. Aganj, J. E. Iglesias, M. Reuter, M. R. Sabuncu, and B. Fischl, “Midspaceindependent deformable image registration,” NeuroImage, vol. 152, pp. 158–170, 2017.  

A.
Gholipour, O. Afacan, I. Aganj, B. Scherrer, S. P.
Prabhu, M. Sahin, and S. K. Warfield, “Superresolution
reconstruction in frequency, image, and wavelet domains to
reduce throughplane partial voluming in MRI,”
Medical Physics, vol. 42, pp. 6919–6932, 2015. 


J. L.
Gaglia, M. Harisinghani, I. Aganj, G. R. Wojtkiewicz,
S. Hedgire, C. Benoist, D. Mathis, and R. Weissleder, “Noninvasive
mapping of pancreatic inflammation in recentonset type1
diabetes patients,”
Proceedings of the National Academy of Sciences, vol.
112, pp. 2139–2144 , 2015. 


I.
Aganj,
M. Reuter, M. R. Sabuncu, and B. Fischl, “Avoiding
symmetrybreaking spatial nonuniformity in deformable image
registration via a quasivolumepreserving constraint,”
NeuroImage, vol. 106, pp. 238–251, 2015. 


J. E.
Iglesias, M. R. Sabuncu, I. Aganj, P. Bhatt, C.
Casillas, D. Salat, A. Boxer, B. Fischl, and K. Van Leemput,
“An
algorithm for optimal fusion of atlases with different
labeling protocols,”
NeuroImage, vol. 106, pp. 451–463, 2015. 


G.
Prasad, S. Joshi, N. Jahanshad, J. Villalon, I. Aganj,
C. Lenglet, G. Sapiro, K. McMahon, G. de Zubicaray, N.
Martin, M. Wright, A. Toga., and P. Thompson, “Automatic
clustering and population analysis of white matter tracts
using maximum density paths,”
NeuroImage, vol. 97, pp. 284–295, 2014. 


I.
Aganj,
B. T. T. Yeo, M. R. Sabuncu, and B. Fischl, “On
removing interpolation and resampling artifacts in rigid
image registration,”
IEEE Transactions on Image Processing, vol. 22, no.
2, pp. 816–827, 2013. 


E.
Caruyer, I. Aganj, C. Lenglet, G. Sapiro, and R.
Deriche, “Motion
detection in diffusion MRI via online ODF estimation,”
International Journal of Biomedical Imaging, vol.
2013, Article ID 849363, 2013. 


I.
Aganj,
C. Lenglet, E. Yacoub, G. Sapiro, and N. Harel, “A
3D wavelet fusion approach for the reconstruction of
isotropicresolution MR images from orthogonal
anisotropicresolution scans,”
Magnetic Resonance in Medicine, vol. 67, no. 4, pp.
1167–1172, 2012. 


I.
Aganj,
C. Lenglet, N. Jahanshad, E. Yacoub, N. Harel, P. Thompson,
and G. Sapiro, “A
Hough transform global probabilistic approach to
multiplesubject diffusion MRI tractography,” Medical
Image Analysis, vol. 15, no. 4, pp. 414–425, 2011. 


I.
Aganj,
C. Lenglet, G. Sapiro, E. Yacoub, K. Ugurbil, and N. Harel,
“Reconstruction
of the orientation distribution function in single and
multiple shell qball imaging within constant solid angle,”
Magnetic Resonance in Medicine, vol. 64, no. 2, pp.
554–566, 2010. 


I.
Aganj,
G. Sapiro, N. Parikshak, S. K. Madsen, and P. Thompson, “Measurement
of cortical thickness from MRI by minimum line integrals on
softclassified tissue,”
Human Brain Mapping, vol. 30, no. 10, pp. 3188–3199,
2009. 


R.
Narasimha, I. Aganj, A. Bennett, M. Borgnia, D.
Zabransky, G. Sapiro, S. McLaughlin, J. Milne, and S.
Subramaniam, “Evaluation
of denoising algorithms for biological electron tomography,”
Journal of Structural Biology, vol. 164, no. 1, pp.
7–17, 2008. 

Book Chapter 



I.
Aganj,
G. Sapiro, and N. Harel, “Qspace
modeling in diffusionweighted MRI,”
in Brain Mapping, A. W. Toga, Ed., Waltham: Academic
Press, 2015, pp. 257–263. 
Conference Articles 


S.
Koley, C. Chakraborty, C. Mainero, B. Fischl, and I.
Aganj, “A
fast approach to automatic detection of brain lesions,”
in Proceedings of the MICCAI Brain Lesions Workshop, Athens,
Greece, 2016. 


Y.
Zhang, I. Aganj, A. van der Kouwe, and M. D. Tisdall,
“Effects
of resolution and registration algorithm on the accuracy of
EPI vNavs for real time head motion correction in MRI,”
in Proceedings of the 7^{th}
International Workshop on Biomedical Image Registration
(held in conjunction with IEEE CVPR),
Las Vegas, NV, 2016. 


I.
Aganj,
J. E. Iglesias, M. Reuter, M. R. Sabuncu, and B. Fischl, “Midspaceindependent
symmetric data term for pairwise deformable image
registration,”
in Proceedings of the 18^{th}
International Conference on Medical Image Computing and
Computer Assisted Intervention,
Munich, Germany, 2015. 


I.
Aganj,
M. Reuter, M. R. Sabuncu, and B. Fischl, “Symmetric
nonrigid image registration via an adaptive
quasivolumepreserving constraint,”
in Proceedings of the IEEE International Symposium on
Biomedical Imaging, 2013. 



A.
Kamath, I. Aganj, J. G. Xu, E. Yacoub, K. Ugurbil, G.
Sapiro, and C. Lenglet, “Generalized
constant solid angle ODF and optimal acquisition protocol
for fiber orientation mapping,”
in Proceedings of the MICCAI Workshop on Computational
Diffusion MRI, Nice, France, 2012. 

E.
Caruyer, I. Aganj, C. Lenglet, G. Sapiro, and R.
Deriche, “Online
motion detection in high angular resolution diffusion
imaging,”
in Proceedings of the Eighth IEEE International Symposium
on Biomedical Imaging, 2011. 


N.
Jahanshad, I. Aganj, C. Lenglet, A. Joshi, Y. Jin, M.
Barysheva, K. McMahon, G. de Zubicaray, N. Martin, M.
Wright, A. Toga, G. Sapiro, and P. Thompson, “Sex
differences in the human connectome: 4Tesla high angular
resolution diffusion imaging (HARDI) tractography in 234
young adult twins,”
in Proceedings of the Eighth IEEE International Symposium
on Biomedical Imaging, 2011. 


G.
Prasad, N. Jahanshad, I. Aganj, C. Lenglet, G.
Sapiro, A. Toga, and P. Thompson, “Atlasbased
fiber clustering for multisubject analysis of high angular
resolution diffusion imaging tractography,”
in Proceedings of the Eighth IEEE International Symposium
on Biomedical Imaging, 2011. 


L.
Zhan, A. Leow, I. Aganj, C. Lenglet, G. Sapiro, E.
Yacoub, N. Harel, A. Toga, and P. Thompson, “Differential
information content in staggered multiple shell HARDI
measured by the tensor distribution function,”
in Proceedings of the Eighth IEEE International Symposium
on Biomedical Imaging, 2011. 


Y.
Jin, Y. Shi, N. Jahanshad, I. Aganj, G. Sapiro, A.
Toga, and P. Thompson, “3D
elastic registration improves HARDIderived fiber alignment
and automated tract clustering,”
in Proceedings of the Eighth IEEE International Symposium
on Biomedical Imaging, 2011. 



G.
Prasad, S. Joshi, N. Jahanshad, J. Villalon, I. Aganj,
C. Lenglet, G. Sapiro, K. McMahon, G. de Zubicaray, N.
Martin, M. Wright, A. Toga, and P. Thompson, “White
matter tract analysis in 454 adults using maximum density
paths,”
in Proceedings of the MICCAI Workshop on Computational
Diffusion MRI, Toronto, Canada, 2011.


I.
Aganj,
C. Lenglet, and G. Sapiro, “ODF
maxima extraction in spherical harmonic representation via
analytical search space reduction,”
in Proceedings of the Thirteenth International Conference
on Medical Image Computing and Computer Assisted
Intervention, pp. 84–91, Beijing, China, 2010. 


E.
Caruyer, I. Aganj, C. Lenglet, G. Sapiro, and R.
Deriche, “Online
orientation distribution function reconstruction in constant
solid angle and its application to motion detection in HARDI,”
in Proceedings of the Seventh IEEE International
Symposium on Biomedical Imaging, Rotterdam, Netherlands,
2010. 


I.
Aganj,
C. Lenglet, G. Sapiro, E. Yacoub, K. Ugurbil, and N. Harel,
“Multiple
qshell ODF reconstruction in qball imaging,”
in Proceedings of the Twelfth International Conference on
Medical Image Computing and Computer Assisted Intervention,
pp. 423–431, London, UK, 2009. 


I.
Aganj,
C. Lenglet, and G. Sapiro, “ODF
reconstruction in qball imaging with solid angle
consideration,”
in Proceedings of the Sixth IEEE International Symposium
on Biomedical Imaging, Boston, MA, 2009. 


I.
Aganj,
G. Sapiro, N. Parikshak, S. K. Madsen, and P. Thompson, “Segmentationfree
measurement of cortical thickness from MRI,”
in Proceedings of the Fifth IEEE International Symposium
on Biomedical Imaging, Paris, France, 2008. 


D.
Rother, K. Patwardhan, I. Aganj, and G. Sapiro, “3D
priors for scene learning from a single view,”
in Proceedings of the IEEE Workshop on Search in 3D (held
in conjunction with CVPR), Anchorage, AK, 2008. 


I.
Aganj,
A. Bartesaghi, M. Borgnia, H.Y. Liao, G. Sapiro, and S.
Subramaniam, “Regularization
for inverting the Radon transform with wedge consideration,”
in Proceedings of the Fourth IEEE International Symposium
on Biomedical Imaging, Arlington, VA, 2007. 


R.
Narasimha, I. Aganj, M. Borgnia, G. Sapiro, S.
McLaughlin, J. Milne, and S. Subramaniam, “From
gigabytes to bytes: Automated denoising and feature
identification in electron tomograms of intact bacterial
cells,”
in Proceedings of the Fourth IEEE International Symposium
on Biomedical Imaging, Arlington, VA, 2007. 

Conference Abstracts 



Y. Zhang, I. Aganj, A. van der Kouwe, and M. D. Tisdall, “Accurate highspeed 3Dregistration of EPI vNavs for head motion correction,” in Proceedings of the Twenty Fifth Annual Meeting of the International Society for Magnetic Resonance in Medicine, Honolulu, HI, 2017. 

I. Aganj,
G. Prasad, P. Srinivasan, A. Yendiki, P. M. Thompson, and B.
Fischl, “Structural
brain network augmentation via Kirchhoff's laws,”
in Proceedings of the Joint Annual Meeting of
ISMRMESMRMB, Milan, Italy, 2014. 


A. Gholipour, O. Afacan, I. Aganj, and S. Warfield, “Superresolution
MRI reconstruction in image, frequency, and wavelet domains,”
in Proc. Joint Annual Meeting of ISMRMESMRMB, Milan,
Italy, 2014. 


G.
Prasad, I. Aganj, and P. Thompson, “Synthesizing
connectivity networks to improve classification of
Alzheimer's disease,” in Proceedings of the 43^{rd}
Annual Meeting of the Society for Neuroscience,
San Diego, CA, 2013. 



A.
Kamath, I. Aganj, J. Xu, E. Yacoub, K. Ugurbil, G.
Sapiro, and C. Lenglet, “Optimal
acquisition protocol for white matter fiber orientation
mapping using generalized CSAODF reconstruction,”
in Proc. Twenty First Annual Meeting of International
Society for Magnetic Resonance in Medicine, 2013. 


G.
Prasad, S. Joshi, N. Jahanshad, J. Villalon, I. Aganj,
C. Lenglet, G. Sapiro, K. McMahon, G. de Zubicaray, N.
Martin, M. Wright, A. Toga, and P. Thompson, “Genetic
analysis of fibers in white matter pathways from HARDI
images,”
in Proceedings of the Eighteenth Annual Meeting of the
Organization for Human Brain Mapping, 2012. 

I.
Aganj,
C. Lenglet, E. Yacoub, G. Sapiro, and N. Harel, “A
wavelet fusion approach to the reconstruction of
isotropicresolution MR images from anisotropic orthogonal
scans,”
in Proceedings of the Nineteenth Annual Meeting of the
International Society for Magnetic Resonance in Medicine,
2011. 


E.
Caruyer, I. Aganj, C. Lenglet, G. Sapiro, and R.
Deriche, “Online
reconstruction and motion detection in HARDI,”
in Proceedings of the Nineteenth Annual Meeting of the
International Society for Magnetic Resonance in Medicine,
2011. 



N.
Jahanshad, I. Aganj, C. Lenglet, G. Sapiro, A. Toga,
K. McMahon, G. de Zubicaray, N. Martin, M. Wright, and P.
Thompson, “4Tesla
high angular resolution diffusion tractography analysis of
the human connectome in 234 subjects: Sex differences and
EPI distortion effects,”
in Proceedings of the Nineteenth Annual Meeting of the
International Society for Magnetic Resonance in Medicine,
2011. 

S. N.
Sotiropoulos, I. Aganj, S. Jbabdi, G. Sapiro, C.
Lenglet, and T. E. Behrens, “Inference on constant solid
angle orientation distribution functions from
diffusionweighted MRI,” in Proceedings of the
Seventeenth Annual Meeting of the Organization for Human
Brain Mapping, 2011. 


G.
Prasad, N. Jahanshad, I. Aganj, C. Lenglet, G.
Sapiro, A. W. Toga, and P. M. Thompson, “Atlasbased
fiber clustering for multisubject HARDI tractography,”
in Proceedings of the Seventeenth Annual Meeting of the
Organization for Human Brain Mapping, 2011. 



L.
Zhan, J. J. GadElkarim, A. D. Leow, I. Aganj, C.
Lenglet, G. Sapiro, N. Harel, A. W. Toga, and P. M.
Thompson, “Probabilistic tractography using the tensor
distribution function in multipleshell HARDI,” in
Proceedings of the Seventeenth Annual Meeting of the
Organization for Human Brain Mapping, 2011. 

I.
Aganj,
N. Jahanshad, C. Lenglet, A. W. Toga, K. L. McMahon, G. I.
de Zubicaray, M. J. Wright, N. G. Martin, G. Sapiro, and P.
Thompson, “Relating
fiber crossing in HARDI to intellectual function,”
in Proceedings of the Sixteenth Annual Meeting of the
Organization for Human Brain Mapping, 2010. 



L.
Zhan, A. D. Leow, I. Aganj, C. Lenglet, G. Sapiro, N.
Harel, A. W. Toga, and P. Thompson, “Tensor
distribution function in multiple shell high angular
resolution diffusion imaging,”
in Proceedings of the Sixteenth Annual Meeting of the
Organization for Human Brain Mapping, 2010. 

I.
Aganj,
C. Lenglet, G. Sapiro, M. C. Chiang, and P. Thompson, “Multisubject
diffusion MRI tractography via a Hough transform global
approach,”
in Proceedings of the Fifteenth Annual Meeting of the
Organization for Human Brain Mapping, 2009. 


I.
Aganj,
C. Lenglet, and G. Sapiro, “Accurate
ODF reconstruction in qball imaging,”
in Proceedings of the Fifteenth Annual Meeting of the
Organization for Human Brain Mapping, 2009. 


I.
Aganj,
C. Lenglet, R. Keriven, G. Sapiro, N. Harel, and P.
Thompson, “A
Hough transform global approach to diffusion MRI
tractography,”
in Proceedings of the Seventeenth Annual Meeting of the
International Society for Magnetic Resonance in Medicine,
2009. 