Dipy protocols

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Dipy specifications

Information


Unique identifier OMICS_23382
Name Dipy
Alternative name Diffusion Imaging in Python
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 0.13.0
Stability Stable
Maintained Yes

Subtool


  • Quickbundles

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Maintainer


  • person_outline Ian Nimmo-Smith <>

Additional information


http://nipy.org/dipy/documentation.html

Publications for Diffusion Imaging in Python

Dipy in pipelines

 (2)
2016
PMCID: 5136564
PMID: 27994537
DOI: 10.3389/fnins.2016.00554

[…] et al. () and with the streamline linear registration (slr) algorithm from garyfallidis et al. (). in all cases, affine registration was applied to streamline coordinates using the function dipy.tracking.streamline.apply_affine(), from dipy. non-linear voxel-level registration was computed with fsl/fnirt, using the deformation fields directly provided within the hcp dataset. gm-based […]

2016
PMCID: 5136564
PMID: 27994537
DOI: 10.3389/fnins.2016.00554

[…] elements equal to one., 7we adopted the software implementation provided by the authors of ent, available at: https://github.com/ljod/whitematteranalysis., 8as implemented in dipy, http://nipy.org/dipy., 9the estimation of the deformation fields of the hcp dataset is described in glasser et al. () in the following way: “after bias field correction of the t1w and t2w images, the t1w image […]


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Dipy in publications

 (18)
PMCID: 5889789
PMID: 29588051
DOI: 10.1016/j.jaac.2018.01.014

[…] was submitted for correction for participant movement and eddy current distortions through the fmrib software library (fsl) eddy tool. next, nonlocal means that de-noising was applied using the diffusion imaging in python (dipy) v0.11 package to boost signal-to-noise ratio. the diffusion tensor model was fitted to the pre-processed images to derive maps of fractional anisotropy (fa) using […]

PMCID: 5803915
PMID: 29415770
DOI: 10.1186/s13195-018-0346-2

[…] epi distortions. then, brain mask, region maps, and tpms were translated from the t2-weighted images to the preprocessed diffusion images. a diffusion tensor model was fitted to the images using dipy [], and fractional anisotropy (fa) was computed. tractography was performed using a deterministic algorithm based on constrained spherical deconvolution model, considering as seed points […]

PMCID: 5808221
PMID: 29467600
DOI: 10.3389/fnins.2017.00754

[…] scikit-learn, see http://scikit-learn.org, and the tractograms in our experiments represented as vectors through the dr., 5the dr of ta is obtained using the prototypes of tb., 6http://nipy.org/dipy., 7https://github.com/demianw/tract_querier., 8http://fsl.fmrib.ox.ac.uk/., 9http://nipy.org/dipy., 10http://scikit-learn.org., 11in case of roc/auc computation, such number varied, in order […]

PMCID: 5677006
PMID: 29116093
DOI: 10.1038/s41467-017-01285-x

[…] scp; 5 mm for cingulum; 6 mm for fornix, icp, or, and uf; 7 mm for fpt, ilf, and popt; 10 mm for cc, mcp, and slf. the full script used to run this bundle recognition implementation was based on the dipy library (www.dipy.org) and is available online (supplementary software )., once vcs are identified, the remaining streamlines can be classified into ics and non-connecting streamlines. […]

PMCID: 5575288
PMID: 28852074
DOI: 10.1038/s41598-017-09915-6

[…] and diffusion tensors were estimated for each voxel using the robust estimation of tensors by outlier rejection (restore) algorithm as part of the diffusion imaging in python (dipy) open source software package. as the largest b-value of the acquisition consisted of 1500 s/mm2, all three shells were utilized in fitting the diffusion tensors. […]


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Dipy institution(s)
Wolfson College, University of Cambridge, Cambridge, UK; Medical Research Council Cognition and Brain Sciences Unit, Cambridge, UK; Henry H. Wheeler Jr. Brain Imaging Center, University of California, Berkeley, CA, USA; Wolfson Brain Imaging Centre, University of Cambridge, Cambridge, UK

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