Iman Aganj's Software page

Structural Brain Connectivity Harmonization Z. Zhou, B. Fischl, and I. Aganj, “Harmonization of structural brain connectivity through distribution matching,” Human Brain Mapping, vol. 46, no. 9:e70257, pp. 1–14, 2025.
	Zhen Zhou’s Matlab implementation.
Intermediate Deformable Image Registration (IDIR) I. Aganj and B. Fischl, “Intermediate deformable image registration via windowed cross-correlation,” in Proceedings of the IEEE International Symposium on Biomedical Imaging, pp. 1–5, Cartagena de Indias, Colombia, 2023.
	The author’s Matlab implementation; see the EXAMPLE_IDIR script.
Expected Label Value (ELV) Computation for Supervised Atlas-Based Image Segmentation I. Aganj and B. Fischl, “Multi-atlas image soft-segmentation via computation of the expected label value,” IEEE Transactions on Medical Imaging, vol. 40, no. 6, pp. 1702–1710, 2021.
	The author’s Matlab implementation; see the EXAMPLE script.
Conductance Model of Brain Connectivity for Diffusion MRI A. Frau-Pascual, M. Fogarty, B. Fischl, A. Yendiki, and I. Aganj, “Quantification of structural brain connectivity via a conductance model,” NeuroImage, vol. 189, pp. 485–496, 2019.
	Aina Frau-Pascual’s Matlab implementation; see: Examples/Connectivity/run_conductance_model.m
Gradient Table Verification in Diffusion MRI I. Aganj, “Automatic verification of the gradient table in diffusion-weighted MRI based on fiber continuity,” Scientific Reports, vol. 8, Article no. 16541, 2018.
	The author’s Matlab implementation (including binaries); see the EXAMPLE routine.
Image Segmentation Based on Local Center of Mass I. Aganj, M. G. Harisinghani, R. Weissleder, and B. Fischl, “Unsupervised medical image segmentation based on the local center of mass,” Scientific Reports, vol. 8, Article no. 13012, 2018.
	The author’s Matlab implementation; see the EXAMPLE script. Also included in the aXonica package.
Segmentation-Based Multimodal Image Registration I. Aganj and B. Fischl, “Multimodal image registration through simultaneous segmentation,” IEEE Signal Processing Letters, vol. 24, no. 11, pp. 1661–1665, 2017.
	The author’s Matlab code; requires SPM12.
	FreeSurfer 7.3’s mri_robust_register command (with --cost SB), implemented in C++ by Reuter et al (NeuroImage, 2010).
Mid-Space-Independent (MSI) Deformable Image Registration I. Aganj, J. E. Iglesias, M. Reuter, M. R. Sabuncu, and B. Fischl, “Mid-space-independent deformable image registration,” NeuroImage, vol. 152, pp. 158–170, 2017.
	The author’s Matlab implementation (including binaries); see the EXAMPLE_MSI script.
Wavelet Image Fusion I. Aganj, C. Lenglet, E. Yacoub, G. Sapiro, and N. Harel, “A 3D wavelet fusion approach for the reconstruction of isotropic-resolution MR images from orthogonal anisotropic-resolution scans,” Magnetic Resonance in Medicine, vol. 67, no. 4, pp. 1167–1172, 2012.
	The author’s Matlab implementation; see the fuseVolW_multi command.
Hough-Transform Tractography I. Aganj, C. Lenglet, N. Jahanshad, E. Yacoub, N. Harel, P. Thompson, and G. Sapiro, “A Hough transform global probabilistic approach to multiple-subject diffusion MRI tractography,” Medical Image Analysis, vol. 15, no. 4, pp. 414–425, 2011.
	The author’s Matlab implementation (including binaries); see the EXAMPLE routine.
Orientation Distribution Function in Constant Solid Angle (CSA-ODF) I. Aganj, C. Lenglet, G. Sapiro, E. Yacoub, K. Ugurbil, and N. Harel, “Reconstruction of the orientation distribution function in single and multiple shell q-ball imaging within constant solid angle,” Magnetic Resonance in Medicine, vol. 64, no. 2, pp. 554–566, 2010.
	The author’s Matlab implementation (including binaries); see the EXAMPLE routine.
	FSL’s qboot command, implemented by Sotiropoulos et al (OHBM, 2011).
	Diffusion Imaging In Python (DIPY)’s CsaOdfModel command, implemented by Garyfallidis et al (Front Neuroinform, 2014). See also Python packages PyNets, Scilpy, and PyAFQ, as well as the GPU implementation in Tractometry.
	MITK Diffusion Imaging’s Q-Ball Reconstruction module, implemented by Fritzsche et al (ISMRM, 2011).
	Ginkgo’s SolidAngleAnalyticalQBallOdf C++ class, developed at NeuroSpin, CEA.
ANIMA	Anima’s animaODFEstimator C function, developed at VisAGeS, Inria.
pHARDI	Parallel High Angular Resolution Diffusion Imaging (pHARDI)’s qbi-csa reconstruction method, implemented by Garcia-Blas et al (ICA3PP, 2016).
dti	R-Package dti’s dwiQball command, implemented by Polzehl and Tabelow (J Stat Softw, 2011). See also the R-Package gdimap.
	HARDI Tools’ test_DOT_R2_vs_CSA_QBI_example Matlab routine, implemented by Canales-Rodríguez et al.
ODF Maxima Extraction 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.
	MITK Diffusion Imaging’s Peak Extraction module, implemented by Fritzsche et al (ISMRM, 2011).
Tissue Thickness Measurement via Minimum Line Integrals I. Aganj, G. Sapiro, N. Parikshak, S. K. Madsen, and P. Thompson, “Measurement of cortical thickness from MRI by minimum line integrals on soft-classified tissue,” Human Brain Mapping, vol. 30, no. 10, pp. 3188–3199, 2009.
	The author’s Matlab / C implementation; see the EXAMPLE routine.
	Atroscan’s cortical thickness analysis solution, implemented by Park et al (Encephalitis, 2023).