Improving the execution performance of FreeSurfer
Delgado, Jordi (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius)
Moure, Juan C. (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius)
Vives-Gilabert, Yolanda (Institut de Física d'Altes Energies)
Delfino, Manuel (Universitat Autònoma de Barcelona. Departament de Física)
Espinosa, Antonio (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius)
Gómez-Ansón, Beatriz (Hospital de la Santa Creu i Sant Pau (Barcelona, Catalunya))
Port d'Informació Científica

Date:	2014
Abstract:	A scheme to significantly speed up the processing of MRI with FreeSurfer (FS) is presented. The scheme is aimed at maximizing the productivity (number of subjects processed per unit time) for the use case of research projects with datasets involving many acquisitions. The scheme combines the already existing GPU-accelerated version of the FS workflow with a task-level parallel scheme supervised by a resource scheduler. This allows for an optimum utilization of the computational power of a given hardware platform while avoiding problems with shortages of platform resources. The scheme can be executed on a wide variety of platforms, as its implementation only involves the script that orchestrates the execution of the workflow components and the FS code itself requires no modifications. The scheme has been implemented and tested on a commodity platform within the reach of most research groups (a personal computer with four cores and an NVIDIA GeForce 480 GTX graphics card). Using the scheduled task-level parallel scheme, a productivity above 0. 6 subjects per hour is achieved on the test platform, corresponding to a speedup of over six times compared to the default CPU-only serial FS workflow.
Grants:	Ministerio de Ciencia e Innovación TIN2011-28689-C02-01
Note:	Altres ajuts: Our work was possible thanks to the cooperation of INNDACYT Association with Port d'Informació Científica (PIC), and Hospital de la Santa Creu i Sant Pau (Barcelona). The Port d'Informació Científica (PIC) is maintained through a collaboration agreement between the Generalitat de Catalunya, CIEMAT, IFAE and the Universitat Autònoma de Barcelona.
Rights:	Tots els drets reservats.
Language:	Anglès
Document:	Article ; recerca ; Versió acceptada per publicar
Subject:	FreeSurfer ; MRI ; Medical imaging ; GPU ; CUDA ; Resource scheduler
Published in:	Neuroinformatics, Vol. 12 (2014) , p. 413-421, ISSN 1559-0089

DOI: 10.1007/s12021-013-9214-1

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