Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Portable simulation framework for diffusion MRI
KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).ORCID iD: 0000-0002-3213-0040
KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).ORCID iD: 0000-0002-1695-8809
Show others and affiliations
2019 (English)In: Journal of magnetic resonance, ISSN 1090-7807, E-ISSN 1096-0856Article in journal (Other (popular science, discussion, etc.)) In press
Abstract [en]

The numerical simulation of the diffusion MRI signal arising from complex tissue micro-structures is helpful for understanding and interpreting imaging data as well as for designing and optimizing MRI sequences. The discretization of the Bloch-Torrey equation by finite elements is a more recently developed approach for this purpose, in contrast to random walk simulations, which has a longer history. While finite elements discretization is more difficult to implement than random walk simulations, the approach benefits from a long history of theoretical and numerical developments by the mathematical and engineering communities. In particular, software packages for the automated solutions of partial differential equations using finite elements discretization, such as FEniCS, are undergoing active support and development. However, because diffusion MRI simulation is a relatively new application area, there is still a gap between the simulation needs of the MRI community and the available tools provided by finite elements software packages. In this paper, we address two potential difficulties in using FEniCS for diffusion MRI simulation. First, we simplified software installation by the use of FEniCS containers that are completely portable across multiple platforms. Second, we provide a portable simulation framework based on Python and whose code is open source. This simulation framework can be seamlessly integrated with cloud computing resources such as Google Colaboratory notebooks working on a web browser or with Google Cloud Platform with MPI parallelization. We show examples illustrating the accuracy, the computational times, and parallel computing capabilities. The framework contributes to reproducible science and open-source software in computational diffusion MRI with the hope that it will help to speed up method developments and stimulate research collaborations.

Place, publisher, year, edition, pages
2019.
Keywords [en]
Cloud computing, diffusion MRI, Bloch-Torrey equation, interface conditions, pseudo-periodic conditions, FEniCS.
National Category
Natural Sciences
Research subject
Applied and Computational Mathematics
Identifiers
URN: urn:nbn:se:kth:diva-256328DOI: 10.1016/j.jmr.2019.106611OAI: oai:DiVA.org:kth-256328DiVA, id: diva2:1344749
Note

QC 20190822

Available from: 2019-08-21 Created: 2019-08-21 Last updated: 2019-09-24

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full texthttps://arxiv.org/abs/1908.01719v1

Authority records BETA

Dancheva, TamaraJansson, JohanHoffman, Johan

Search in DiVA

By author/editor
Nguyen, Van DangLeoni, MassimilianoDancheva, TamaraJansson, JohanHoffman, Johan
By organisation
Computational Science and Technology (CST)
In the same journal
Journal of magnetic resonance
Natural Sciences

Search outside of DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 24 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf