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Dipy, a library for the analysis of diffusion MRI data
2014
Frontiers in Neuroinformatics
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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
2017
Frontiers in Neuroinformatics
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., 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]
2020
arXiv
pre-print
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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]
2021
bioRxiv
pre-print
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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]
2021
bioRxiv
pre-print
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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]
2021
bioRxiv
pre-print
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, 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
2011
Frontiers in Neuroinformatics
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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
2021
Aperture Neuro
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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]
2020
bioRxiv
pre-print
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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]
2014
Mathematics and Visualization
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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]
2019
bioRxiv
pre-print
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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
2022
Journal of Clinical Medicine
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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
2019
Quantitative Imaging in Medicine and Surgery
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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]
2017
Mathematics and Visualization
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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
2017
BMC Medical Imaging
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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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