Sökning: WFRF:(Jansson Johan) >
Portable simulation...
Portable simulation framework for diffusion MRI
-
- Nguyen, Van Dang, 1985- (författare)
- KTH,Beräkningsvetenskap och beräkningsteknik (CST)
-
- Leoni, Massimiliano (författare)
- KTH,Beräkningsvetenskap och beräkningsteknik (CST)
-
- Dancheva, Tamara (författare)
- KTH,Beräkningsvetenskap och beräkningsteknik (CST)
-
visa fler...
-
- Jansson, Johan (författare)
- KTH,Beräkningsvetenskap och beräkningsteknik (CST)
-
- Hoffman, Johan, 1974- (författare)
- KTH,Beräkningsvetenskap och beräkningsteknik (CST)
-
Wassermann, Demian (författare)
-
Li, Jing-Rebecca (författare)
-
visa färre...
-
(creator_code:org_t)
- Academic Press, 2019
- 2019
- Engelska.
-
Ingår i: Journal of magnetic resonance. - : Academic Press. - 1090-7807 .- 1096-0856. ; 309
- Relaterad länk:
-
https://bird.bcamath...
-
visa fler...
-
https://urn.kb.se/re...
-
https://doi.org/10.1...
-
visa färre...
Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- NATURVETENSKAP -- Matematik (hsv//swe)
- NATURAL SCIENCES -- Mathematics (hsv//eng)
Nyckelord
- Cloud computing
- diffusion MRI
- Bloch-Torrey equation
- interface conditions
- pseudo-periodic conditions
- FEniCS.
- Tillämpad matematik och beräkningsmatematik
- Applied and Computational Mathematics
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
Hitta via bibliotek
Till lärosätets databas