Matched-filter acquisition for bold fMRI

NeuroImage

Volumn 100, Issue , 2014, Pages 145-160

  Kasper, Lars ^a   Haeberlin, Maximilian ^a   Dietrich, Benjamin E ^a   Gross, Simon ^a   Barmet, Christoph ^a,b   Wilm, Bertram J ^a   Vannesjo, S Johanna ^a   Brunner, David O ^a   Ruff, Christian C ^c   Stephan, Klaas E ^a,c   Pruessmann, Klaas P ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b Skope Magnetic Resonance Technologies   (Switzerland)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Bold sensitivity; Density weighted epi; FMRI; Image smoothing; Magnetic field monitoring; Matched filter

Indexed keywords

ARTICLE; BOLD SIGNAL; CONTRAST SENSITIVITY; ECHO PLANAR IMAGING; FEASIBILITY STUDY; FUNCTIONAL MAGNETIC RESONANCE IMAGING; HUMAN; HUMAN EXPERIMENT; IMAGE PROCESSING; IMAGE QUALITY; IMAGE RECONSTRUCTION; IMAGE SMOOTHING; INFORMATION PROCESSING; KERNEL METHOD; MAGNETIC FIELD; MATCHED FILTER ACQUISITION; PRIORITY JOURNAL; SIGNAL NOISE RATIO; SIGNAL PROCESSING; TWO DIMENSIONAL ECHOCARDIOGRAPHY; ADULT; NUCLEAR MAGNETIC RESONANCE IMAGING; PHYSIOLOGY; PROCEDURES; STATISTICAL ANALYSIS; VISUAL CORTEX;

ADULT; CONTRAST SENSITIVITY; DATA INTERPRETATION, STATISTICAL; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MAGNETIC RESONANCE IMAGING; SIGNAL-TO-NOISE RATIO; VISUAL CORTEX;

EID: 84903894048     PISSN: 10538119     EISSN: 10959572     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2014.05.024     Document Type: Article

References (70)

1. Ahn C.B., Kim J.H., Cho Z.H. High-speed spiral-scan echo planar NMR imaging-I. IEEE Trans. Med. Imaging 1986, 5:2-7. 10.1109/TMI.1986.4307732.
2. Andrade A., Kherif F., Mangin J.-F., Worsley K.J., Paradis A.-L., Simon O., Dehaene S., Le Bihan D., Poline J.-B. Detection of fMRI activation using cortical surface mapping. Hum. Brain Mapp. 2001, 12:79-93. 10.1002/1097-0193(200102)12:2<79::AID-HBM1005>3.0.CO;2-I.
3. Barmet C., De Zanche N., Pruessmann K.P. Spatiotemporal magnetic field monitoring for MR. Magn. Reson. Med. 2008, 60:187-197.
4. Barmet C., De Zanche N., Wilm B.J., Pruessmann K.P. A transmit/receive system for magnetic field monitoring of in vivo MRI. Magn. Reson. Med. 2009, 62:269-276. 10.1002/mrm.21996.
5. Barmet C., Wilm B.J., Pavan M., Katsikatsos G., Keupp J., Mens G., Pruessmann K.P. Concurrent higher-order field monitoring for routine head MRI: an integrated heteronuclear setup. Proc. Intl. Soc. Mag. Reson. Med. 2010, 18:216.
6. Barmet C., Wilm B.J., Kasper L., Ruff C.C., Stephan K.E., Pruessmann K.P. fMRI with concurrent magnetic field monitoring. Proc. Intl. Soc. Mag. Reson. Med. 2011, 19:3609.
7. Beatty P.J., Nishimura D.G., Pauly J.M. Rapid gridding reconstruction with a minimal oversampling ratio. IEEE Trans. Med. Imaging 2005, 24:799-808.
8. Bianciardi M., Fukunaga M., van Gelderen P., Horovitz S.G., de Zwart J.A., Shmueli K., Duyn J.H. Sources of functional magnetic resonance imaging signal fluctuations in the human brain at rest: a 7T study. Magn. Reson. Imaging 2009, 27:1019-1029. 10.1016/j.mri.2009.02.004.
9. Birn R.M., Smith M.A., Jones T.B., Bandettini P.A. The respiration response function: the temporal dynamics of fMRI signal fluctuations related to changes in respiration. NeuroImage 2008, 40:644-654. 10.1016/j.neuroimage.2007.11.059.
10. Biswal B., Zerrin Yetkin F., Haughton V.M., Hyde J.S. Functional connectivity in the motor cortex of resting human brain using echo-planar MRI. Magn. Reson. Med. 1995, 34:537-541. 10.1002/mrm.1910340409.
11. Börnert P., Schomberg H., Aldefeld B., Groen J. Improvements in spiral MR imaging. Magn. Reson. Mater. Phys. Biol. Med. 1999, 9:29-41. 10.1007/BF02634590.
12. Buckner R.L., Krienen F.M., Yeo B.T.T. Opportunities and limitations of intrinsic functional connectivity MRI. Nat. Neurosci. 2013, 16:832-837. 10.1038/nn.3423.
13. Carp J. The secret lives of experiments: methods reporting in the fMRI literature. NeuroImage 2012, 63:289-300. 10.1016/j.neuroimage.2012.07.004.
14. Chang C., Glover G.H. Variable-density spiral-in/out functional magnetic resonance imaging. Magn. Reson. Med. 2011, 65:1287-1296. 10.1002/mrm.22722.
15. Chang C., Cunningham J.P., Glover G.H. Influence of heart rate on the BOLD signal: the cardiac response function. NeuroImage 2009, 44:857-869. 10.1016/j.neuroimage.2008.09.029.
16. Cole D.M., Smith S.M., Beckmann C.F. Advances and pitfalls in the analysis and interpretation of resting-state fMRI data. Front. Syst. Neurosci. 2010, 4:1-15. 10.3389/fnsys.2010.00008.
17. Dagli M.S., Ingeholm J.E., Haxby J.V. Localization of cardiac-induced signal change in fMRI. NeuroImage 1999, 9:407-415. 10.1006/nimg.1998.0424.
18. De Zanche N., Barmet C., Nordmeyer-Massner J.A., Pruessmann K.P. NMR probes for measuring magnetic fields and field dynamics in MR systems. Magn. Reson. Med. 2008, 60:176-186.
19. Friston K.J. Chapter 2 - Statistical parametric mapping. Statistical Parametric Mapping 2007, 10-31. Academic Press, London. K.J. Friston, J. Ashburner, S. Kiebel, T. Nichols, W. Penny (Eds.).
20. Glover G.H., Lai S. Self-navigated spiral fMRI: interleaved versus single-shot. Magn. Reson. Med. 1998, 39:361-368. 10.1002/mrm.1910390305.
21. Glover G.H., Li T.Q., Ress D. Image-based method for retrospective correction of physiological motion effects in fMRI: RETROICOR. Magn. Reson. Med. 2000, 44:162-167. (doi:10893535).
22. Goense J., Merkle H., Logothetis N.K. High-resolution fMRI reveals laminar differences in neurovascular coupling between positive and negative BOLD responses. Neuron 2012, 76:629-639. 10.1016/j.neuron.2012.09.019.
23. Graedel N.N., Vannesjo S.J., Kasper L., Gross S., Dietrich B.E., Barmet C., Pruessmann K.P. Image Reconstruction Using the Gradient Impulse Response for Trajectory Prediction. Presented at the ISMRM, Salt Lake City, USA 2013, 552.
24. Greiser A., von Kienlin M. Efficient k-space sampling by density-weighted phase-encoding. Magn. Reson. Med. 2003, 50:1266-1275. 10.1002/mrm.10647.
25. Greiser A., Haase A., von Kienlin M. Improved cardiac sodium MR imaging by density-weighted phase-encoding. J. Magn. Reson. Imaging 2005, 21:78-81. 10.1002/jmri.20237.
26. Hall J. Linear Deming Regression - File Exchange - MATLAB Central [WWW Document] 2011, (URL http://www.mathworks.com/matlabcentral/fileexchange/file_infos/33484-linear-deming-regression (accessed 8.16.13)).
27. Harrison L.M., Penny W., Flandin G., Ruff C.C., Weiskopf N., Friston K.J. Graph-partitioned spatial priors for functional magnetic resonance images. NeuroImage 2008, 43:694-707. 10.1016/j.neuroimage.2008.08.012.
28. Harvey A.K., Pattinson K.T.S., Brooks J.C.W., Mayhew S.D., Jenkinson M., Wise R.G. Brainstem functional magnetic resonance imaging: disentangling signal from physiological noise. J. Magn. Reson. Imaging 2008, 28:1337-1344. 10.1002/jmri.21623.
29. Haynes J.-D., Rees G. Decoding mental states from brain activity in humans. Nat. Rev. Neurosci. 2006, 7:523-534. 10.1038/nrn1931.
30. Hutton C., Josephs O., Stadler J., Featherstone E., Reid A., Speck O., Bernarding J., Weiskopf N. The impact of physiological noise correction on fMRI at 7T. NeuroImage 2011, 57:101-112. 10.1016/j.neuroimage.2011.04.018.
31. Jackson J.I., Meyer C.H., Nishimura D.G., Macovski A. Selection of a convolution function for Fourier inversion using gridding. IEEE Trans. Med. Imaging 1991, 10:473-478. 10.1109/42.97598.
32. Johnson J.B. Thermal agitation of electricity in conductors. Phys. Rev. 1928, 32:97-109. 10.1103/PhysRev.32.97.
33. Kasper L., Marti S., Vannesjö S.J., Hutton C., Dolan R., Weiskopf N., Stephan K.E., Prüssmann K.P. Cardiac Artefact Correction for Human Brainstem fMRI at 7 Tesla. Proceedings of the Organization for Human Brain Mapping 2009, 15:395.
34. Kasper L., Vannesjo S.J., Haeberlin M., Barmet C., Stephan K.E., Pruessmann K.P. Non-uniform density EPI acquisition improves the SNR of smoothed MR images. Proc. Intl. Soc. Mag. Reson. Med. 2010, 18:3040.
35. Kasper L., Haeberlin M., Wilm B.J., Stephan K.E., Pruessmann K.P. 2D Matched-filter Acquisition for Improved SNR in Routine Brain Imaging. Proc. Intl. Soc. Mag. Reson. Med. 2012, 20:2299.
36. Kim D., Adalsteinsson E., Spielman D.M. Simple analytic variable density spiral design. Magn. Reson. Med. 2003, 50:214-219. 10.1002/mrm.10493.
37. Kimmlingen R., Eberlein E., Dietz P., Kreher S., Schuster J., Riegler J., Matschl V., Schnetter V., Schmidt A., Lenz H., Mustafa E., Fischer D., Potthast A., Kreischer L., Eberler M., Hebrank F., Thein H., Heberlein K., Hoecht P., Witzel T., Tisdall D., Xu J., Yacoub E., Adriany G., Auerbach E., Moeller S., Feinberg D., Lehne D., Wald L.L., Rosen B., Ugurbil K., Essen, D.van, Wedeen V., Schmitt F. Concept and realization of high strength gradients for the Human Connectome Project. Proc. Intl. Soc. Mag. Reson. Med. 2012, 20:696.
38. Koopmans P.J., Barth M., Norris D.G. Layer-specific BOLD activation in human V1. Hum. Brain Mapp. 2010, 31:1297-1304. 10.1002/hbm.20936.
39. Krüger G., Glover G.H. Physiological noise in oxygenation-sensitive magnetic resonance imaging. Magn. Reson. Med. 2001, 46:631-637. 10.1002/mrm.1240.
40. Lindquist M.A., Wager T.D. Spatial smoothing in fMRI using prolate spheroidal wave functions. Hum. Brain Mapp. 2008, 29:1276-1287. 10.1002/hbm.20475.
41. Lustig M., Kim S.-J., Pauly J.M. A fast method for designing time-optimal gradient waveforms for arbitrary k-Space trajectories. IEEE Trans. Med. Imaging 2008, 27:866-873. 10.1109/TMI.2008.922699.
42. Lutti A., Thomas D.L., Hutton C., Weiskopf N. High-resolution functional MRI at 3T: 3D/2D echo-planar imaging with optimized physiological noise correction. Magn. Reson. Med. 2013, 69:1657-1664. 10.1002/mrm.24398.
43. Man L.C., Pauly J.M., Macovski A. Multifrequency interpolation for fast off-resonance correction. Magn. Reson. Med. 1997, 37:785-792. (doi:9126954).
44. North D.O. An Analysis of the factors which determine signal/noise discrimination in pulsed-carrier systems. Proc. IEEE 1963, 51:1016-1027. 10.1109/PROC.1963.2383.
45. Nyquist H. Thermal agitation of electric charge in conductors. Phys. Rev. 1928, 32:110-113. 10.1103/PhysRev.32.110.
46. Pipe J., Duerk J.L. Analytical resolution and noise characteristics of linearly reconstructed magnetic resonance data with arbitrary k-space sampling. Magn. Reson. Med. 1995, 34:170-178. 10.1002/mrm.1910340207.
47. Poldrack R.A., Fletcher P.C., Henson R.N., Worsley K.J., Brett M., Nichols T.E. Guidelines for reporting an fMRI study. NeuroImage 2008, 40:409-414. 10.1016/j.neuroimage.2007.11.048.
48. Poser B.A., Koopmans P.J., Witzel T., Wald L.L., Barth M. Three dimensional echo-planar imaging at 7 Tesla. NeuroImage 2010, 51:261-266. 10.1016/j.neuroimage.2010.01.108.
49. Pruessmann, K., Tsao, J., 2008. United States Patent: 7342397 - Magnetic resonance imaging method. 7342397.
50. Pruessmann K.P., Weiger M., Börnert P., Boesiger P. Advances in sensitivity encoding with arbitrary k-space trajectories. Magn. Reson. Med. 2001, 46:638-651. 10.1002/mrm.1241.
51. Salvado O., Hillenbrand C., Zhang S., Wilson D.L. Method to correct intensity inhomogeneity in MR images for atherosclerosis characterization. IEEE Trans. Med. Imaging 2006, 25:539-552. 10.1109/TMI.2006.871418.
52. Shmueli K., van Gelderen P., de Zwart J.A., Horovitz S.G., Fukunaga M., Martijn Jansma J., Duyn J.H. Low frequency fluctuations in the cardiac rate as a source of variance in the resting-state fMRI BOLD signal. NeuroImage 2007, 38:306-320. 10.1016/j.neuroimage.2007.07.037.
53. Spielman D.M., Pauly J.M., Meyer C.H. Magnetic resonance fluoroscopy using spirals with variable sampling densities. Magn. Reson. Med. 1995, 34:388-394. 10.1002/mrm.1910340316.
54. Stobbe R., Beaulieu C. Advantage of sampling density weighted apodization over postacquisition filtering apodization for sodium MRI of the human brain. Magn. Reson. Med. 2008, 60:981-986. 10.1002/mrm.21738.
55. Sutton B.P., Noll D.C., Fessler J.A. Fast, iterative image reconstruction for MRI in the presence of field inhomogeneities. IEEE Trans. Med. Imaging 2003, 22:178-188. 10.1109/TMI.2002.808360.
56. Tabelow K., Polzehl J., Voss H.U., Spokoiny V. Analyzing fMRI experiments with structural adaptive smoothing procedures. NeuroImage 2006, 33:55-62. 10.1016/j.neuroimage.2006.06.029.
57. Triantafyllou C., Hoge R.D., Wald L.L. Effect of spatial smoothing on physiological noise in high-resolution fMRI. NeuroImage 2006, 32:551-557. 10.1016/j.neuroimage.2006.04.182.
58. Van De Ville D., Blu T., Unser M. Surfing the brain. IEEE Eng. Med. Biol. Mag. 2006, 25:65.
59. Van Essen D.C., Ugurbil K., Auerbach E., Barch D., Behrens T.E.J., Bucholz R., Chang A., Chen L., Corbetta M., Curtiss S.W., Della Penna S., Feinberg D., Glasser M.F., Harel N., Heath A.C., Larson-Prior L., Marcus D., Michalareas G., Moeller S., Oostenveld R., Petersen S.E., Prior F., Schlaggar B.L., Smith S.M., Snyder A.Z., Xu J., Yacoub E. The Human Connectome Project: A data acquisition perspective. NeuroImage 2012, 62:2222-2231. 10.1016/j.neuroimage.2012.02.018.
60. Vannesjo S.J., Dietrich B.E., Pavan M., Brunner D.O., Wilm B.J., Barmet C., Pruessmann K.P. Field camera measurements of gradient and shim impulse responses using frequency sweeps. Magn. Reson. Med 2013, 10.1002/mrm.24934.
61. Vannesjo S.J., Haeberlin M., Kasper L., Pavan M., Wilm B.J., Barmet C., Pruessmann K.P. Gradient system characterization by impulse response measurements with a dynamic field camera. Magn. Reson. Med. 2013, 69:583-593. 10.1002/mrm.24263.
62. Weisstein E.W. "Parseval's theorem." From MathWorld-A Wolfram Web Resource. [WWW Document] 2006, URL http://mathworld.wolfram.com/ParsevalsTheorem.html (accessed 6.27.13b).
63. Weisstein E.W. "Wiener-Khinchin theorem." From MathWorld-A Wolfram Web Resource. [WWW Document] 2006, URL http://mathworld.wolfram.com/Wiener-KhinchinTheorem.html (accessed 6.27.13a).
64. Wilm B.J., Barmet C., Pavan M., Pruessmann K.P. Higher order reconstruction for MRI in the presence of spatiotemporal field perturbations. Magn. Reson. Med. 2011, 65:1690-1701. 10.1002/mrm.22767.
65. Wilm B.J., Barmet C., Pruessmann K.P. Fast higher-order MR image reconstruction using singular-vector separation. IEEE Trans. Med. Imaging 2012, 31:1396-1403. 10.1109/TMI.2012.2190991.
66. Worsley K.J., Marrett S., Neelin P., Evans A.C. Searching scale space for activation in PET images. Hum. Brain Mapp. 1996, 4:74-90. (4:1<74::AID-HBM5>3.0.CO;2-M). 10.1002/(SICI)1097-0193(1996).
67. Worsley K.J., Marrett S., Neelin P., Vandal A.C., Friston K.J., Evans A.C. A unified statistical approach for determining significant signals in images of cerebral activation. Hum. Brain Mapp. 1996, 4:58-73. (4:1<58::AID-HBM4>3.0.CO;2-O). 10.1002/(SICI)1097-0193(1996).
68. Yang Q.X., Lindquist M.A., Shepp L., Zhang Cun-Hui, Wang J., Smith M.B. Two dimensional prolate spheroidal wave functions for MRI. J. Magn. Reson. 2002, 158:43-51. 10.1016/S1090-7807(02)00058-7.
69. Zahneisen B., Hugger T., Lee K.J., LeVan P., Reisert M., Lee H.-L., Assländer J., Zaitsev M., Hennig J. Single shot concentric shells trajectories for ultra fast fMRI. Magn. Reson. Med. 2012, 68:484-494. 10.1002/mrm.23256.
70. Zeller M., Müller A., Gutberlet M., Nichols T., Hahn D., Köstler H., Bartsch A.J. Boosting BOLD fMRI by k-space density weighted echo planar Imaging. PLoS ONE 2013, 8:e74501. 10.1371/journal.pone.0074501.