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Dipy, a library for the analysis of diffusion MRI data

Eleftherios Garyfallidis, Matthew Brett, Bagrat Amirbekian, Ariel Rokem, Stefan van der Walt, Maxime Descoteaux, Ian Nimmo-Smith
2014 Frontiers in Neuroinformatics  
Copyright statement: ABSTRACT Diffusion Imaging in Python (Dipy) is a free and open source software project for the analysis of data from diffusion magnetic resonance imaging (dMRI) experiments. dMRI is  ...  Dipy aims to provide transparent implementations for all the different steps of dMRI analysis with a uniform programming interface.  ...  Dipy provides a number of simple-to-use methods for the analysis of diffusion MRI data using the Python language.  ... 
doi:10.3389/fninf.2014.00008 pmid:24600385 pmcid:PMC3931231 fatcat:fx54hqnslrb3th6l46q3caavfy

Pypes: Workflows for Processing Multimodal Neuroimaging Data

Alexandre M. Savio, Michael Schutte, Manuel Graña, Igor Yakushev
2017 Frontiers in Neuroinformatics  
., 2008) is used from Dipy for image de-noising with a Rician filter.  ...  Pypes gives support to the growing community of researchers having access to hybrid PET/MRI scanners which require complex proprocessing and analysis of multimodal imaging data.  ... 
doi:10.3389/fninf.2017.00025 pmid:28443013 pmcid:PMC5387693 fatcat:g37bgt5loveqxjdqy32kkeskiq

TRAKO: Efficient Transmission of Tractography Data for Visualization [article]

Daniel Haehn, Loraine Franke, Fan Zhang, Suheyla Cetin Karayumak, Steve Pieper, Lauren O'Donnell, Yogesh Rathi
2020 arXiv   pre-print
We integrate a state-of-the-art compression technique for vertices, streamlines, and attached scalar and property data.  ...  Such vast amounts of data require formats that allow for efficient storage, transfer, and visualization.  ...  TRAKO reduces data sizes by a factor of 10-28x with an average error that is lower than the voxel size of the original diffusion MRI.  ... 
arXiv:2004.13630v1 fatcat:fyqqmjom55ac7cziav2tmozjpm

Diffusional Kurtosis Imaging in the Diffusion Imaging in Python Project [article]

Rafael Neto Henriques, Marta Morgado Correia, Maurizio Maralle, Elizabeth Huber, John Kruper, Serge Koudoro, Jason D Yeatman, Eleftherios Garyfallidis, Ariel Rokem
2021 bioRxiv   pre-print
Diffusional Kurtosis Imaging (DKI) quantifies the degree of non-Gaussian diffusion in biological tissue from dMRI.  ...  In summary, DKI in DIPY provides a well-tested, well-documented and comprehensive reference implementation for DKI.  ...  DIPY is an open-source software library that provides implementations of many different methods for analysis of dMRI data (Garyfallidis et al., 2014) .  ... 
doi:10.1101/2021.03.04.433972 fatcat:vflv4u2xy5e63dnai33brcj2ny

Evaluating the reliability of human brain white matter tractometry [article]

John Kruper, Jason D Yeatman, Adam Richie-Halford, David Bloom, Mareike Grotheer, Sendy Caffarra, Gregory Kiar, Iliana I Karipidis, Ethan Roy, Ariel Rokem
2021 bioRxiv   pre-print
In recent years, there have been concerns about the validity of research that uses diffusion-weighted MRI (dMRI) to understand human brain white matter connections in vivo, in part based on reliability  ...  The validity of research results depends on the reliability of analysis methods.  ...  The WU-Minn Human Connectome Project (HCP) (88) includes measurements of diffusion MRI data from almost all of the 1,200 participants.  ... 
doi:10.1101/2021.02.24.432740 fatcat:qv2x7mimoreqlcpvlnkiwejazy

mrHARDIflow : A pipeline tailored for the preprocessing and analysis of Multi-Resolution High Angular diffusion MRI and its application to a variability study of the PRIME-DE database [article]

Alex Valcourt Caron, Amir Shmuel, Ziqi Hao, Maxime Descoteaux
2021 bioRxiv   pre-print
, tailored for the analysis of diffusion data acquired on multiple spatial resolutions.  ...  Modules of processes and workflows were implemented upon cutting edge and state-of-the-art MRI processing technologies and diffusion modelling algorithms, namely Diffusion Tensor Imaging (DTI), Constrained  ...  Usability and Reproducibility The libraries used for diffusion MRI are ever-changing.  ... 
doi:10.1101/2021.11.22.469616 fatcat:4u4cqj2kmjc4jo6bk76csrhwxm

The Connectome Viewer Toolkit: An Open Source Framework to Manage, Analyze, and Visualize Connectomes

Stephan Gerhard, Alessandro Daducci, Alia Lemkaddem, Reto Meuli, Jean-Philippe Thiran, Patric Hagmann
2011 Frontiers in Neuroinformatics  
On the macroscale level of description, diffusion-weighted magnetic resonance imaging (MRI) is the main imaging technology employed for mapping the structural connectivity of the human connectome (Hagmann  ...  The efficiency of sharing data and source code would benefit if a transdisciplinary lingua franca for programming was available.  ...  For Diffusion MRI, Dipy implements reconstruction, tractography, and fiber visualization methods in a free and open source manner.  ... 
doi:10.3389/fninf.2011.00003 pmid:21713110 pmcid:PMC3112315 fatcat:stufldro4zaahfx3x5hzfawvs4

Evaluating the Reliability of Human Brain White Matter Tractometry

John Kruper, Jason D. Yeatman, Adam Richie-Halford, David Bloom, Mareike Grotheer, Sendy Caffarra, Gregory Kiar, Iliana I. Karipidis, Ethan Roy, Bramsh Q. Chandio, Eleftherios Garyfallidis, Ariel Rokem
2021 Aperture Neuro  
In recent years, there have been concerns about the validity of research that uses diffusion-weighted MRI (dMRI) to understand human brain white matter connections in vivo, in part based on the reliability  ...  The validity of research results depends on the reliability of analysis methods.  ...  This pipeline is a full end-to-end pipeline and system for deployment of analysis that receives as input raw MRI data as acquired on the scanner.  ... 
doi:10.52294/e6198273-b8e3-4b63-babb-6e6b0da10669 pmid:35079748 pmcid:PMC8785971 fatcat:rytvwmjxiffedd6qcoxgr3ptum

Neurobiological underpinnings of rapid white matter plasticity during intensive reading instruction [article]

Elizabeth Huber, Aviv Mezer, Jason Yeatman
2020 bioRxiv   pre-print
Behavioral measures, multi-shell diffusion MRI data, and quantitative T1 data were collected at regular intervals during the intervention in a group of 33 children with reading difficulties (7-12 years  ...  Yet it is challenging to infer the biological underpinnings of this plasticity using non-invasive measurements like diffusion MRI.  ...  "Dipy, a library for the analysis of diffusion MRI (7321): 244-252. Novikov, D. S., V. G. Kiselev and S. N. Jespersen (2018). "On modeling." Magn Reson Med 79(6): 3172-3193.  ... 
doi:10.1101/2020.05.28.122499 fatcat:qmy232lvivgirdlkqjs4kzekye

Motion Is Inevitable: The Impact of Motion Correction Schemes on HARDI Reconstructions [chapter]

Shireen Elhabian, Yaniv Gur, Clement Vachet, Joseph Piven, Martin Styner, Ilana Leppert, G. Bruce Pike, Guido Gerig
2014 Mathematics and Visualization  
Given the necessity for rigorous quality control and motion correction, users are often left to use simple heuristics to select correction schemes, but do not fully understand the consequences of such  ...  choices on the final analysis, moreover being at risk to introduce confounding factors in population studies.  ...  Full brain tractography was performed using the EuDX deterministic tracking technique [14] (implemented in the DiPy library), using random seeding inside the brain region and a turning-angle threshold  ... 
doi:10.1007/978-3-319-11182-7_15 fatcat:oqqptf6i2bcergrj2bwtjlebyq

Apparent Propagator Anisotropy from reduced Diffusion MRI acquisitions [article]

Santiago Aja-Fernandez, Antonio Tristan-Vega, Derek Jones
2019 bioRxiv   pre-print
The Propagator Anisotropy (PA) is a measurement of the orientational variability inside a tissue estimated from diffusion MRI using the Ensemble Average diffusion Propagator (EAP).  ...  However, the use of PA is not generalized among the clinical community, due to the great amount of data needed for its calculation, together with the associated long processing times.  ...  The authors thank the contributors of DIPY project (http://nipy.org/dipy/) for providing the MAP-MRI basis implementation and specially to Rutger Fick for his implementation for PA calculation and interesting  ... 
doi:10.1101/798892 fatcat:zfw2dgzp4rgn5aekraobygtc34

Quantitative MR Markers in Non-Myelopathic Spinal Cord Compression: A Narrative Review

Jan Valošek, Petr Bednařík, Miloš Keřkovský, Petr Hluštík, Josef Bednařík, Alena Svátková
2022 Journal of Clinical Medicine  
Thus, we aim to review the ability of qMRI techniques (such as diffusion MRI, diffusion tensor imaging (DTI), magnetization transfer (MT) imaging, and magnetic resonance spectroscopy (1H-MRS)) to serve  ...  markers of DCM development for accurate patient management.  ...  Acknowledgments: We thank Eva Vlčková, from University Hospital Brno, for her rigorous revisions of the text and for providing valuable advice.  ... 
doi:10.3390/jcm11092301 pmid:35566426 pmcid:PMC9105390 fatcat:6ehgkard5bbvznf3qxeec5edle

IMAge/enGINE: a freely available software for rapid computation of high-dimensional quantification

Ming Yang, Yaping Yan, He Wang
2019 Quantitative Imaging in Medicine and Surgery  
It processes the high-dimensional image data in a slice-by-slice computation mechanism.  ...  The architecture of IMAge/enGINE is modularized for easier extension.  ...  Footnote Conflicts of Interest: The authors have no conflicts of interest to declare.  ... 
doi:10.21037/qims.2018.12.03 pmid:30976545 pmcid:PMC6414769 fatcat:lh3gjx7jgvc4vfih43e6tdyo7i

Repeated Tractography of a Single Subject: How High Is the Variance? [chapter]

Xuan Gu, Anders Eklund, Hans Knutsson
2017 Mathematics and Visualization  
We have investigated the test-retest reliability of diffusion tractography, using 32 diffusion datasets from a single healthy subject.  ...  Preprocessing was carried out using functions in FSL (FMRIB Software Library), and tractography was carried out using FSL and Dipy.  ...  the Swedish Research Council (grant 2015-05356, "Learning of sets of diffusion MRI sequences for optimal imaging of micro structures").  ... 
doi:10.1007/978-3-319-61358-1_14 fatcat:6c6xtnpopjb7hpdegyeh7ktijm

Improving the evaluation of cardiac function in rats at 7T with denoising filters: a comparison study

Benoit Tricot, Maxime Descoteaux, Matthieu Dumont, Frederic Chagnon, Luc Tremblay, André Carpentier, Olivier Lesur, Martin Lepage, Alain Lalande
2017 BMC Medical Imaging  
The performance of the ORNLM filter was superior for all the parameters of the cardiac function, as judged from the inter-and intra-observer variabilities.  ...  Series were denoised with an anisotropic diffusion filter, a whole variation regularization or an optimized Rician non-local means (ORNLM) filtering technique.  ...  Background Magnetic Resonance Imaging (MRI) is a valuable tool for the detection of cardiovascular diseases.  ... 
doi:10.1186/s12880-017-0236-2 pmid:29258458 pmcid:PMC5735834 fatcat:yxgrnkpsevgyljtahka43g52ra
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