STAMPS: Software Tool for Automated MRI Post-processing on a supercomputer

Don C. Bigler; Yaman Aksu; David Jonathan Miller; Qing Yang

doi:10.1016/j.cmpb.2009.02.006

STAMPS: Software Tool for Automated MRI Post-processing on a supercomputer

Don C. Bigler
, Yaman Aksu
, David Jonathan Miller
, Qing Yang

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

This paper describes a Software Tool for Automated MRI Post-processing (STAMP) of multiple types of brain MRIs on a workstation and for parallel processing on a supercomputer (STAMPS). This software tool enables the automation of nonlinear registration for a large image set and for multiple MR image types. The tool uses standard brain MRI post-processing tools (such as SPM, FSL, and HAMMER) for multiple MR image types in a pipeline fashion. It also contains novel MRI post-processing features. The STAMP image outputs can be used to perform brain analysis using Statistical Parametric Mapping (SPM) or single-/multi-image modality brain analysis using Support Vector Machines (SVMs). Since STAMPS is PBS-based, the supercomputer may be a multi-node computer cluster or one of the latest multi-core computers.

Original language	English (US)
Pages (from-to)	146-157
Number of pages	12
Journal	Computer Methods and Programs in Biomedicine
Volume	95
Issue number	2
DOIs	https://doi.org/10.1016/j.cmpb.2009.02.006
State	Published - Aug 2009

All Science Journal Classification (ASJC) codes

Software
Computer Science Applications
Health Informatics

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10.1016/j.cmpb.2009.02.006

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@article{a6722ab7e847484885e95a5a4b2b433a,

title = "STAMPS: Software Tool for Automated MRI Post-processing on a supercomputer",

abstract = "This paper describes a Software Tool for Automated MRI Post-processing (STAMP) of multiple types of brain MRIs on a workstation and for parallel processing on a supercomputer (STAMPS). This software tool enables the automation of nonlinear registration for a large image set and for multiple MR image types. The tool uses standard brain MRI post-processing tools (such as SPM, FSL, and HAMMER) for multiple MR image types in a pipeline fashion. It also contains novel MRI post-processing features. The STAMP image outputs can be used to perform brain analysis using Statistical Parametric Mapping (SPM) or single-/multi-image modality brain analysis using Support Vector Machines (SVMs). Since STAMPS is PBS-based, the supercomputer may be a multi-node computer cluster or one of the latest multi-core computers.",

author = "Bigler, \{Don C.\} and Yaman Aksu and Miller, \{David Jonathan\} and Qing Yang",

note = "Funding Information: This work was supported in part by the NIH (RO1 EB00454 and 1R01AG027771-01A2), The Zimmerman Family Love Fund, The Paul and Harriett Campbell ALS Research Fund, and The ALS Association, Greater Philadelphia Chapter. ",

year = "2009",

month = aug,

doi = "10.1016/j.cmpb.2009.02.006",

language = "English (US)",

volume = "95",

pages = "146--157",

journal = "Computer Methods and Programs in Biomedicine",

issn = "0169-2607",

publisher = "Elsevier Ireland Ltd",

number = "2",

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T2 - Software Tool for Automated MRI Post-processing on a supercomputer

AU - Bigler, Don C.

AU - Aksu, Yaman

AU - Miller, David Jonathan

AU - Yang, Qing

N1 - Funding Information: This work was supported in part by the NIH (RO1 EB00454 and 1R01AG027771-01A2), The Zimmerman Family Love Fund, The Paul and Harriett Campbell ALS Research Fund, and The ALS Association, Greater Philadelphia Chapter.

PY - 2009/8

Y1 - 2009/8

N2 - This paper describes a Software Tool for Automated MRI Post-processing (STAMP) of multiple types of brain MRIs on a workstation and for parallel processing on a supercomputer (STAMPS). This software tool enables the automation of nonlinear registration for a large image set and for multiple MR image types. The tool uses standard brain MRI post-processing tools (such as SPM, FSL, and HAMMER) for multiple MR image types in a pipeline fashion. It also contains novel MRI post-processing features. The STAMP image outputs can be used to perform brain analysis using Statistical Parametric Mapping (SPM) or single-/multi-image modality brain analysis using Support Vector Machines (SVMs). Since STAMPS is PBS-based, the supercomputer may be a multi-node computer cluster or one of the latest multi-core computers.

AB - This paper describes a Software Tool for Automated MRI Post-processing (STAMP) of multiple types of brain MRIs on a workstation and for parallel processing on a supercomputer (STAMPS). This software tool enables the automation of nonlinear registration for a large image set and for multiple MR image types. The tool uses standard brain MRI post-processing tools (such as SPM, FSL, and HAMMER) for multiple MR image types in a pipeline fashion. It also contains novel MRI post-processing features. The STAMP image outputs can be used to perform brain analysis using Statistical Parametric Mapping (SPM) or single-/multi-image modality brain analysis using Support Vector Machines (SVMs). Since STAMPS is PBS-based, the supercomputer may be a multi-node computer cluster or one of the latest multi-core computers.

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DO - 10.1016/j.cmpb.2009.02.006

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SN - 0169-2607

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JO - Computer Methods and Programs in Biomedicine

JF - Computer Methods and Programs in Biomedicine

IS - 2

ER -

STAMPS: Software Tool for Automated MRI Post-processing on a supercomputer

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