Youtube Gallery

Introduction to computational neuroanatomy

Talk by Dr. Wei Tang of Indiana University, Department of Computer Science. Synopsis Dr. Tang will explain the basic terminology ...

Matrix Sketching for Patch2Self - Part 3

This video explains matrix sketching and how it is used for Patch2Self to speed up regression, implicitly reducing memory footprint ...

Noise Uncertainty Quantification (NUQ) Metric - Part 4

This video explains a new metric to evaluate denoising performance on Diffusion MRI data using Uncertainty Quantification.

Introduction and Welcome

Talk by Prof. Garyfallidis of Indiana University, Department of Intelligent Systems Engineering. Garyfallidis is the Workshop Chair, ...

Focus on Q-Space Trajectory Imaging (QTI) - part1

Talk by Dr. Kerkela of University College London, United Kingdom and Dr. Henriques of the Champalimaud Center of the ...

Diffusion Tensor Imaging (DTI)

Talk by Dr. Ariel Rokem of University of Washington, Seattle. Dr. Rokem is Associate DIPY Lead and a long-time contributor to the ...

Diffusion Kurtosis Imaging (DKI)

Talk by Dr. Henriques of the Champalimaud Center of Unknown, Portugal. Synopsis Dr. Henriques will explain Kurtosis Imaging ...

Denoising Introduction - Part 1

This video explains the outline of Shreyas Fadnavis's talks via a short overview of denoising approaches. More information on: ...

Brain Extraction using V-Net and CRF layers

This video explains the using V-Net with Conditional Random Field to do brain extraction in T1 modalities. More information on: ...

Visualization

Talk by Eng. Javier Guaje of Indiana University, Department of Intelligent Systems Engineering. Guaje is one of the lead ...

Diffusion Kurtosis Imaging (DKI) - Practice

Talk by Dr. Henriques of the Champalimaud Center of Unknown, Portugal. Synopsis Dr. Henriques will explain Kurtosis Imaging ...

Spherical harmonic-based reconstruction

Talk by: a) Prof. Descoteaux of University of Sherbrooke, Department of Computer Science, Canada. Prof. Descoteaux is the ...

Patch2Self Denoising of Diffusion MRI - Part 2

Explains the Patch2Self denoising approach in detail with practical implementation in DIPY. Refer to: Fadnavis, Shreyas, Joshua ...

Focus on Q-Space Trajectory Imaging (QTI) - part 2 - Practise

Talk by Dr. Kerkela of University College London, United Kingdom and Dr. Henriques of the Champalimaud Center of the ...

Tractometry and Bundle Analytics

Talk by Bramsh Chandio, PhD Candidate in the Dept of Intelligent Systems Engineering at Indiana University Bloomington.

Optimization constraints for dMRI

Presented by Tom Dela Haije Prof. Haije of the University of Copenhagen will talk about his recent invention to improve the ...

Image Registration - Part 3 - Non Linear Registration

Talk by Serge Koudoro, Indiana University. Mr. Koudoro is the release manager for DIPY. He is a software engineer with great ...

Tractometry Part 3 - BUAN - Bundle Shape Similarity Analysis

Talk by Bramsh Chandio, PhD Candidate in the Dept of Intelligent Systems Engineering at Indiana University Bloomington.

Image Registration - Part 1 - Basic Concepts

Talk by Serge Koudoro, Indiana University. Mr. Koudoro is the release manager for DIPY. He is a software engineer with great ...

Tissue Classification - A classic approach

More information on: https://dipy.org or https://dipy.org/workshops/dipy-workshop-2022 Please cite: --------------- Garyfallidis E, Brett ...

Parallel Transport Tractography

Presented by Baran Aydogan Prof. Baran Aydogan from Eastern Finland university will talk about Parallel Transport Tractography ...

Tractometry Part 4 - BUAN - Demo on Parkinson’s data

Talk by Bramsh Chandio, PhD Candidate in the Dept of Intelligent Systems Engineering at Indiana University Bloomington.

Unsupervised Tractography Segmentation

Dr. Eleftherios Garyfallidis, DIPY Lead and creator, Assistant Professor of Intelligent Systems Engineering at Indiana University ...

Deep learning for white matter parcellation

Presented by Lauren J. O'Donnell Prof. Lauren O'Donnell from Harvard will talk about the recently proposed deep learning ...

RUMBA-SD Model

Presented by Kenji Marshall and Erick Jorge Canales-Rodriguez Synopsis Dr. Canales-Rodriguez is the inventor of RUMBA-SD.

Gallery

../../_images/data.png Getting started with DIPY
../../_images/tractogram_EuDX.png Introduction to Basic Tracking
../../_images/gradients.png Gradients and Spheres
../../_images/median_otsu.png Brain segmentation with median_otsu
../../_images/CC_segmentation.png SNR estimation for Diffusion-Weighted Images
../../_images/denoised_patch2self.png Patch2Self: Self-Supervised Denoising via Statistical Independence
../../_images/denoised.png Denoise images using Non-Local Means (NLMEANS)
../../_images/denoised_localpca.png Denoise images using Local PCA via empirical thresholds
../../_images/pca_sigma.png Denoise images using the Marcenko-Pastur PCA algorithm
../../_images/Gibbs_suppression_msdki.png Suppress Gibbs oscillations
../../_images/csd_both.png Reconstruction with Constrained Spherical Deconvolution
../../_images/msdodf.png Reconstruction with Multi-Shell Multi-Tissue CSD
../../_images/fODFs.png Crossing invariant fiber response function with FORECAST model
../../_images/odfs.png Continuous and analytical diffusion signal modelling with 3D-SHORE
../../_images/SHORE_maps.png Calculate SHORE scalar maps
../../_images/odfs.png Continuous and analytical diffusion signal modelling with MAP-MRI
../../_images/qt_indices_rtpp.png Estimating diffusion time dependent q-space indices using qt-dMRI
../../_images/tensor_odfs.png Reconstruction of the diffusion signal with the Tensor model
../../_images/dti_fa_distributions.png Using the RESTORE algorithm for robust tensor fitting
../../_images/In_vivo_free_water_DTI_and_standard_DTI_corrected.png Using the free water elimination model to remove DTI free water contamination
../../_images/Measures_from_kurtosis_tensor_only.png Reconstruction of the diffusion signal with the kurtosis tensor model
../../_images/MSDKI_simulations.png Mean signal diffusion kurtosis imaging (MSDKI)
../../_images/Kurtosis_Microstructural_measures.png Reconstruction of the diffusion signal with the WMTI model
../../_images/csa_odfs.png Reconstruct with Constant Solid Angle (Q-Ball)
../../_images/dsi_gfa.png Reconstruct with Diffusion Spectrum Imaging
../../_images/msd.png Calculate DSI-based scalar maps
../../_images/dsid.png DSI Deconvolution vs DSI
../../_images/sf_both.png Reconstruction with the Sparse Fascicle Model
../../_images/diffusion_coeff.png Intravoxel incoherent motion
../../_images/model_predictions.png K-fold cross-validation for model comparison
../../_images/asym_reconst_full.png Signal Reconstruction Using Spherical Harmonics
../../_images/rumba_global_peaks.png Reconstruction with Robust and Unbiased Model-BAsed Spherical Deconvolution
../../_images/enhancements.png Crossing-preserving contextual enhancement
../../_images/OR_after.png Fiber to bundle coherence measures
../../_images/tractogram_EuDX.png Introduction to Basic Tracking
../../_images/tractogram_deterministic_dg.png An introduction to the Deterministic Maximum Direction Getter
../../_images/tractogram_probabilistic_dg_sh_pfm.png An introduction to the Probabilistic Direction Getter
../../_images/tractogram_closest_peak_dg.png Bootstrap and Closest Peak Direction Getters Example
../../_images/tractogram_deterministic_act_valid.png Using Various Stopping Criterion for Tractography
../../_images/tractogram_probabilistic_cmc.png Particle Filtering Tractography
../../_images/tractogram_sfm.png Tracking with the Sparse Fascicle Model
../../_images/tractogram_probabilistic_rumba.png Tracking with Robust Unbiased Model-BAsed Spherical Deconvolution (RUMBA-SD)
../../_images/spatial_errors.png Linear fascicle evaluation (LiFE)
../../_images/surface_seed2.png Surface seeding for tractography
../../_images/connectivity.png Connectivity Matrices, ROI Intersections and Density Maps
../../_images/lengths_plots.png Streamline length and size reduction
../../_images/filtered_cci_streamlines.png Calculation of Outliers with Cluster Confidence Index
../../_images/Path_Length_Map.png Calculate Path Length Map
../../_images/tract_profiles.png Extracting AFQ tract profiles from segmented bundles
../../_images/af_l_after_assignment_maps.png BUAN Bundle Assignment Maps Creation
../../_images/two_bundles.png BUAN Bundle Shape Similarity Score
../../_images/xformed_dwi_2.png Affine Registration in 3D
../../_images/series_mask_2.png Affine Registration with Masks
../../_images/diffeomorphic_map_b0s.png Symmetric Diffeomorphic Registration in 2D
../../_images/warped_static.png Symmetric Diffeomorphic Registration in 3D
../../_images/map-3.png Diffeomorphic Registration with binary and fuzzy images
../../_images/after_registration.png Direct Bundle Registration
../../_images/after_group_registration.png Groupwise Bundle Registration
../../_images/transformed_axial.png Applying image-based deformations to streamlines
../../_images/fornix_clusters.png Tractography Clustering with QuickBundles
../../_images/fornix_clusters_cosine.png Enhancing QuickBundles with different metrics and features
../../_images/vector_of_endpoints_feature.png Tractography Clustering - Available Features
../../_images/cosine_metric.png Tractography Clustering - Available Metrics
../../_images/median_otsu.png Brain segmentation with median_otsu
../../_images/probabilities.png Tissue Classification of a T1-weighted Structural Image
../../_images/CST_L_refine_recognized_bundle.png Automatic Fiber Bundle Extraction with RecoBundles
../../_images/multi_tensor_simulation.png MultiTensor Simulation
../../_images/dsid.png DSI Deconvolution vs DSI
../../_images/simulated_dki_signal.png DKI MultiTensor Simulation
../../_images/bundles_and_3_slices.png Advanced interactive visualization
../../_images/mosaic.png Simple volume slicing
../../_images/bundle6.png Visualize bundles and metrics on bundles
../../_images/contour_from_roi_tutorial.png Visualization of ROI Surface Rendered with Streamlines
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