Intermediate Deformable Image Registration (IDIR)

The author’s Matlab implementation; see the EXAMPLE_IDIR script.

Expected Label Value (ELV) Computation for Supervised Atlas-Based Image Segmentation

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

The author’s Matlab implementation; see the EXAMPLE script.

Segmentation-Based Multimodal Image Registration

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

The author’s Matlab implementation (including binaries); see the EXAMPLE_MSI script.

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 and Scilpy.

MITK Diffusion Imaging’s Q-Ball Reconstruction module, implemented by Fritzsche et al (ISMRM, 2011).

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).

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.