fMRat: an extension of SPM for a fully automatic analysis of rodent brain functional magnetic resonance series.
The purpose of this study was to develop a multi-platform automatic software tool for full processing of fMRI rodent studies. Existing tools require the usage of several different plug-ins, a significant user interaction and/or programming skills. Based on a user-friendly interface, the tool provide...
| Publicado en: | Medical & Biological Engineering & Computing Vol. 54; no. 5; pp. 743 - 753 |
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| Autores principales: | , , , , , |
| Formato: | pictorial research tables/charts Journal Article |
| Publicado: |
Springer Nature
May2016
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=114606457&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 114606457 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 01400118 PO0 jtl: Medical & Biological Engineering & Computing issn: 01400118 maglogo: N pubinfo: dt: May2016 vid: 54 iid: 5 pid: 237 pub: Springer Nature place: New York, New York artinfo: ui: 114606457 114606457 NLM26285671 114606457 10.1007/s11517-015-1365-9 NLM26285671 114606457 ppf: 743 ppct: 10 formats: fmt: @attributes: type: P tig: atl: fMRat: an extension of SPM for a fully automatic analysis of rodent brain functional magnetic resonance series. aug: au: Chavarrías, Cristina García-Vázquez, Verónica Alemán-Gómez, Yasser Montesinos, Paula Pascau, Javier Desco, Manuel Chavarrías, Cristina García-Vázquez, Verónica Alemán-Gómez, Yasser affil: Instituto de Investigación Sanitaria Gregorio Marañón, Doctor Esquerdo 46 28007 Madrid Spain sug: subj: Algorithms Magnetic Resonance Imaging Methods Brain Physiology Rats Computer Graphics User-Computer Interface Animal Studies Validation Studies Comparative Studies Evaluation Research Multicenter Studies ab: The purpose of this study was to develop a multi-platform automatic software tool for full processing of fMRI rodent studies. Existing tools require the usage of several different plug-ins, a significant user interaction and/or programming skills. Based on a user-friendly interface, the tool provides statistical parametric brain maps (t and Z) and percentage of signal change for user-provided regions of interest. The tool is coded in MATLAB (MathWorks(®)) and implemented as a plug-in for SPM (Statistical Parametric Mapping, the Wellcome Trust Centre for Neuroimaging). The automatic pipeline loads default parameters that are appropriate for preclinical studies and processes multiple subjects in batch mode (from images in either Nifti or raw Bruker format). In advanced mode, all processing steps can be selected or deselected and executed independently. Processing parameters and workflow were optimized for rat studies and assessed using 460 male-rat fMRI series on which we tested five smoothing kernel sizes and three different hemodynamic models. A smoothing kernel of FWHM = 1.2 mm (four times the voxel size) yielded the highest t values at the somatosensorial primary cortex, and a boxcar response function provided the lowest residual variance after fitting. fMRat offers the features of a thorough SPM-based analysis combined with the functionality of several SPM extensions in a single automatic pipeline with a user-friendly interface. The code and sample images can be downloaded from https://github.com/HGGM-LIM/fmrat . pubtype: Academic Journal doctype: pictorial research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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