Skip to main content
SpringerLink
Log in

fMRat: an extension of SPM for a fully automatic analysis of rodent brain functional magnetic resonance series

  • Original Article
  • Published:
Medical & Biological Engineering & Computing Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

Abbreviations

SPM:

Statistical Parametric Mapping

fMRI:

Functional magnetic resonance imaging

FWHM:

Full width at half maximum

BOLD:

Blood-oxygen-level-dependent

GLM:

General linear model

HRF:

Hemodynamic response function

ROI:

Region of interest

GUI:

Graphical user interface

TR:

Repetition time

TE:

Echo time

FOV:

Field of view

(SE-)EPI:

(Spin echo) echo planar imaging

RARE:

Rapid acquisition with relaxation enhancement

S1FL:

Primary somatosensorial cortex forelimb region left

S1FR:

Primary somatosensorial cortex forelimb region right

S1HL:

Primary somatosensorial cortex hindlimb region left

S1HR:

Primary somatosensorial cortex hindlimb region right

SNR:

Signal-to-noise ratio

References

  1. Brett M, Anton J, Valabregue R, Poline J (2002) Region of interest analysis using an SPM toolbox. Neuroimage 16(2 Suppl 1):769–1198

    Google Scholar 

  2. Bruker Biospin Paravision 5.0 Users Manual. Bruker AXS GmbH, Germany

  3. Carp J (2012) The secret lives of experiments: methods reporting in the fMRI literature. Neuroimage 63:289–300

    Article  PubMed  Google Scholar 

  4. Chen BR, Bouchard MB, McCaslin AFH, Burgess SA, Hillman EMC (2011) High-speed vascular dynamics of the hemodynamic response. NeuroImage 54:1021–1030

    Article  PubMed  PubMed Central  Google Scholar 

  5. Cox RW, Ashburner JRW, Breman H, Fissell F, Haselgrove C, Holmes CJ, Lancaster JL, Rex DE, Smith SM, Woodward JB, Strother SC (2004) A (sort of) new image data format standard: Nifti-1. OHBM meeting

  6. Draganski B, Gaser C, Kempermann G, Kuhn HG, Winkler J, Büchel C, May A (2006) Temporal and Spatial Dynamics of Brain Structure Changes during Extensive Learning. The Journal of Neuroscience 26:6314–6317

    Article  CAS  PubMed  Google Scholar 

  7. Friston KJ, Ashburner J, Frith C, Poline JB, Heather JD, Frackowiak RSJ (1995) Spatial registration and normalization of images. Hum Brain Mapp 2:165–189

    Article  Google Scholar 

  8. Friston KJ, Williams S, Howard R, Frackowiak RSJ, Turner R (1996) Movement-related effects in fMRI time-series. Magn Reson Med 35:346–355

    Article  CAS  PubMed  Google Scholar 

  9. Friston KJ, Penny W, Phillips C, Kiebel S, Hinton G, Ashburner J (2002) Classical and bayesian inference in neuroimaging: theory. NeuroImage 16:465–483

    Article  CAS  PubMed  Google Scholar 

  10. Friston KJ, Ashburner J, Kiebel S, Nichols T, Penny W (2007) Statistical parametric mapping: the analysis of functional brain images. Academic Press, Elsevier, London

    Book  Google Scholar 

  11. Gyngell ML, Bock C, Schmitz B, Hoehn-Berlage M, Hossmann KA (1996) Variation of functional MRI signal in response to frequency of somatosensory stimulation in alpha-chloralose anesthetized rats. Magn Reson Med 36:13–15

    Article  CAS  PubMed  Google Scholar 

  12. Hill D, Studholme C, Hawkes D (1994) Voxel similarity measures for automated image registration. Proc Med Imaging 2359:205–216

    Google Scholar 

  13. Hyder F, Behar K, Martin M, Shulman R (1993) Activation of the somatosensory motor cortex in anesthetized rats during forepaw stimulation localized by magnetic resonance imaging. Soc Magn Reson Med 3:379

    Google Scholar 

  14. Hyder F, Behar KL, Martin MA, Blamire AM, Shulman RG (1994) Dynamic magnetic resonance imaging of the rat brain during forepaw stimulation. J Cereb Blood Flow Metab 14:649–655

    Article  CAS  PubMed  Google Scholar 

  15. Johnson GA, Calabrese E, Badea A, Paxinos G, Watson C (2012) A multidimensional magnetic resonance histology atlas of the Wistar rat brain. NeuroImage 62:1848–1856

    Article  PubMed  PubMed Central  Google Scholar 

  16. Logothetis NK (2008) What we can do and what we cannot do with fMRI. Nature 453:869–878

    Article  CAS  PubMed  Google Scholar 

  17. Logothetis NK, Pfeuffer J (2004) On the nature of the BOLD fMRI contrast mechanism. Magn Reson Imaging 22:1517–1531

    Article  PubMed  Google Scholar 

  18. Martin C, Martindale J, Berwick J, Mayhew J (2006) Investigating neural–hemodynamic coupling and the hemodynamic response function in the awake rat. NeuroImage 32:33–48

    Article  PubMed  Google Scholar 

  19. Paxinos G, Watson CR, Emson PC (1980) AChE-stained horizontal sections of the rat brain in stereotaxic coordinates. J Neurosci Methods 3:129–149

    Article  CAS  PubMed  Google Scholar 

  20. Sawiak SJ, Wood NI, Williams GB, Morton AJ, Carpenter TA (2009) Voxel-based morphometry in the R6/2 transgenic mouse reveals differences between genotypes not seen with manual 2D morphometry. Neurobiol Dis 33:20–27

    Article  CAS  PubMed  Google Scholar 

  21. Schwarz A, Danckaert A, Reese T, Gozzi A, Paxinos G, Watson C, Merlo-Pich E, Bifone A (2006) A stereotaxic MRI template set for the rat brain with tissue class distribution maps and co-registered anatomical atlas: application to pharmacological MRI. NeuroImage 32:538–550

    Article  PubMed  Google Scholar 

  22. Silva AC, Koretsky AP (2002) Laminar specificity of functional MRI onset times during somatosensory stimulation in rat. Proc Natl Acad Sci USA 99:15182–15187

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Strupp JP (1996) Stimulate: a GUI based fMRI analysis software package. NeuroImage 3:S607

    Article  Google Scholar 

  24. Weber R, Ramos-Cabrer P, Wiedermann D, van Camp N, Hoehn M (2006) A fully noninvasive and robust experimental protocol for longitudinal fMRI studies in the rat. Neuroimage 29:1303–1310

    Article  PubMed  Google Scholar 

  25. Worsley KJ, Friston KJ (1995) Analysis of fMRI time-series revisited-again. NeuroImage 2:173–181

    Article  CAS  PubMed  Google Scholar 

  26. Zong X, Lee J, John Poplawsky A, Kim S-G, Ye JC (2014) Compressed sensing fMRI using gradient-recalled echo and EPI sequences. NeuroImage 92:312–321

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was funded in part by grants from Ministerio de Economía y Competitividad (PI10/02986) and Red Cardiovascular (RD12/0042/0057). The authors would like to thank Alexandra de Francisco López and Yolanda Sierra Palomares for their excellent work in animal preparation and handling.

Authors’ contributions

C.C. implemented the tool, performed the experiments for the evaluation, analyzed the datasets and wrote the manuscript; V.G.V. and Y.A.G. helped with the implementation regarding SPM package; P.M. helped with the MRI data acquisition; J.P. collaborated in the software engineering; and M.D. collaborated in the design, coordinated all the workflow and helped to draft, write and review the manuscript. All authors read and approved the final manuscript.

Author information

Authors and Affiliations

  1. Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Avda. de la Universidad 30, 28911, Leganés, Madrid, Spain

    Cristina Chavarrías, Verónica García-Vázquez, Yasser Alemán-Gómez, Javier Pascau & Manuel Desco

  2. Instituto de Investigación Sanitaria Gregorio Marañón, Doctor Esquerdo 46, 28007, Madrid, Spain

    Cristina Chavarrías, Verónica García-Vázquez, Yasser Alemán-Gómez, Paula Montesinos, Javier Pascau & Manuel Desco

  3. Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain

    Manuel Desco

Authors
  1. Cristina Chavarrías
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Verónica García-Vázquez
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yasser Alemán-Gómez
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Paula Montesinos
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Javier Pascau
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Manuel Desco
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Cristina Chavarrías.

Ethics declarations

Competing interests

The authors have declared that they have no competing interests.

Statement of ethical approval

Animals were handled according to the European Communities Council Directive (2010/63/UE) and national regulations (RD 53/2013) and with the approval of the Animal Experimentation Ethics Committee of Hospital General Universitario Gregorio Marañón.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chavarrías, C., García-Vázquez, V., Alemán-Gómez, Y. et al. fMRat: an extension of SPM for a fully automatic analysis of rodent brain functional magnetic resonance series. Med Biol Eng Comput 54, 743–752 (2016). https://doi.org/10.1007/s11517-015-1365-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11517-015-1365-9

Keywords

Search

Navigation