Literature (Narrative) Review

Some Points to Consider in a Task-Based fMRI Study: A Guideline for Beginners

Abstract

Functional Magnetic Resonance Imaging (fMRI) is a technique widely used to probe brain function, and has shown many research and clinical applications. Despite its popularity and strength, performing an fMRI study needs careful consideration of the design of the experiment, as well as the techniques and methodologies implemented in it, due to the high potential of these factors to alter the outputs of the study. The influences of the demographics of the participants, stimuli design, image acquisition, and data analysis methods on the fMRI results are illustrated previously. Therefore, it is of utmost significance to have an understanding of the critical considerations when designing an fMRI study. In this manuscript, by reviewing the methodology of over one hundred task-based fMRI studies, around 300 substantial tips regarding the different stages of an fMRI experiment are gathered. These could only be found scattered through the literature, and such a collection would act as a guideline for the beginners in the field of fMRI. 

1- G. H. Glover, “Overview of Functional Magnetic Resonance Imaging,” Neurosurg. Clin. N. Am., vol. 22, no. 2, pp. 133–139, Apr. 2011.
2- P. S. Sachdev, T. Lee, W. Wen, D. Ames, A. H. Batouli, J. Bowden, H. Brodaty, E. Chong, J. Crawford, K. Kang, K. Mather, A. Lammel, M. J. Slavin, A. Thalamuthu, J. Trollor, and M. J. Wright, “The contribution of twins to the study of cognitive ageing and dementia: The Older Australian Twins Study,” Int. Rev. Psychiatry, vol. 25, no. 6, pp. 738–747, Dec. 2013.
3- A. Zare Sadeghi, A. H. Jafari, M. A. Oghabian, H. R. Salighehrad, S. A. H. Batouli, S. Raminfard, and H. Ekhtiari, “Changes in Effective Connectivity Network Patterns in Drug Abusers, Treated With Different Methods,” Basic Clin. Neurosci., vol. 8, no. 4, pp. 285–298, Sep. 2017.
4- R. Alemi, S. A. H. Batouli, E. Behzad, M. Ebrahimpoor, and M. A. Oghabian, “Not single brain areas but a network is involved in language: Applications in presurgical planning,” Clin. Neurol. Neurosurg., vol. 165, pp. 116–128, 2018.
5- M. Fakhri, H. Sikaroodi, F. Maleki, M. Ali Oghabian, and H. Ghanaati, “Age-Related Frontal Hyperactivation Observed across Different Working Memory Tasks: An fMRI Study,” Behav. Neurol., vol. 25, no. 4, pp. 351–361, Aug. 2012.
6- S. A. H. Batouli and M. Sisakhti, “Investigating A Hypothesis on The Mechanism of Long-Term Memory Storage,” NeuroQuantology; Vol 17, No 3, Mar. 2019.
7- S. A. H. Batouli and V. Saba, “At least eighty percent of brain grey matter is modifiable by physical activity: A review study,” Behav. Brain Res., vol. 332, no. Supplement C, pp. 204–217, 2017.
8- S. A. H. Batouli, N. Hasani, S. Gheisari, E. Behzad, and M. A. Oghabian, “Evaluation of the factors influencing brain language laterality in presurgical planning,” Phys. Medica, vol. 32, no. 10, pp. 1201–1209, Dec. 2016.
9- H. Parker, C. L. Hoad, E. Tucker, C. Costigan, L. Marciani, P. Gowland, and M. Fox, “Gastric motor and sensory function in health assessed by magnetic resonance imaging: Establishment of reference intervals for the Nottingham test meal in healthy subjects,” Neurogastroenterol. Motil., vol. 0, no. 0, p. e13463, Sep. 2018.
10- A. Schindler and A. Bartels, “Human V6 Integrates Visual and Extra-Retinal Cues during Head-Induced Gaze Shifts,” iScience, vol. 7, pp. 191–197, Sep. 2018.
11- N. H. Neufeld, B. H. Mulsant, E. W. Dickie, B. S. Meyers, G. S. Alexopoulos, A. J. Rothschild, E. M. Whyte, M. J. Hoptman, A. Nazeri, J. Downar, A. J. Flint, and A. N. Voineskos, “Resting state functional connectivity in patients with remitted psychotic depression: A multi-centre STOP-PD study,” EBioMedicine, 2018.
12- G. Li, P. Liu, E. Andari, A. Zhang, and K. Zhang, “The Role of Amygdala in Patients With Euthymic Bipolar Disorder During Resting State,” Front. Psychiatry, vol. 9, p. 445, Sep. 2018.
13- M. Oghabian and S. Batouli, “Using functional magnetic resonance imaging to differentiate between healthy aging subjects, Mild Cognitive Impairment, and Alzheimer’s patients,” J. Res. …, vol. 15, no. 2, pp. 84–93, 2010.
14- S. A. H. Batouli, A. Boroomand, M. Fakhri, H. Sikaroodi, M. A. Oghabian, and K. Firouznia, “The Effect of Aging on Resting State Brain Function: An fMRI Study,” Iran. J. Radiol., vol. 6, no. 3, pp. 153–158, 2009.
15- C. He, Y. Chen, T. Jian, H. Chen, X. Guo, J. Wang, L. Wu, H. Chen, and X. Duan, “Dynamic functional connectivity analysis reveals decreased variability of the default-mode network in developing autistic brain,” Autism Res., vol. 0, no. 0, Oct. 2018.
16- B. Klugah-Brown, C. Luo, H. He, S. Jiang, G. K. Armah, Y. Wu, J. Li, W. Yin, and D. Yao, “Altered Dynamic Functional Network Connectivity in Frontal Lobe Epilepsy,” Brain Topogr., 2018.
17- F. Tomaiuolo, L. Cecchetti, R. M. Gibson, F. Logi, A. M. Owen, F. Malasoma, S. Cozza, P. Pietrini, and E. Ricciardi, “Progression from Vegetative to Minimally Conscious State Is Associated with Changes in Brain Neural Response to Passive Tasks: A Longitudinal Single-Case Functional MRI Study,” J. Int. Neuropsychol. Soc., vol. 22, no. 6, pp. 620–630, 2016.
18- M. D. Greicius, G. Srivastava, A. L. Reiss, and V. Menon, “Default-mode network activity distinguishes Alzheimer’s disease from healthy aging: Evidence from functional MRI,” Proc. Natl. Acad. Sci. U. S. A., vol. 101, no. 13, pp. 4637–4642, Mar. 2004.
19- T. L. Richards and V. W. Berninger, “Abnormal fMRI Connectivity in Children with Dyslexia During a Phoneme Task: Before But Not After Treatment .,” J. Neurolinguistics, vol. 21, no. 4, pp. 294–304, Jul. 2008.
20- R. G. Wise and C. Preston, “What is the value of human FMRI in CNS drug development?,” Drug Discov. Today, vol. 15, no. 21, pp. 973–980, 2010.
21- M. Fakhri, M. A. Oghabian, F. Vedaei, A. Zandieh, N. Masoom, G. Sharifi, M. Ghodsi, and K. Firouznia, “Atypical Language Lateralization: an fMRI study in patients with cerebral lesions,” Funct. Neurol., vol. 28, no. 1, pp. 55–61, 2013.
22- D. Zacà, J. Nickerson, G. Deib, and J. Pillai, “Effectiveness of four different clinical fMRI paradigms for preoperative regional determination of language lateralization in patients with brain tumors,” Neuroradiology, vol. 54, no. 9, pp. 1015–1025, 2012.
23- B. Weber, J. Wellmer, S. Schür, V. Dinkelacker, J. Ruhlmann, F. Mormann, N. Axmacher, C. E. Elger, and G. Fernández, “Presurgical language fMRI in patients with drug-resistant epilepsy: effects of task performance.,” Epilepsia, vol. 47, no. 5, pp. 880–6, May 2006.
24- M. Caulo, R. Esposito, D. Mantini, C. Briganti, C. Sestieri, P. a Mattei, C. Colosimo, G. L. Romani, and a Tartaro, “Comparison of hypothesis- and a novel hybrid data/hypothesis-driven method of functional MR imaging analysis in patients with brain gliomas.,” AJNR. Am. J. Neuroradiol., vol. 32, no. 6, pp. 1056–64, 2011.
25- C. Rosazza, F. Ghielmetti, L. Minati, P. Vitali, a R. Giovagnoli, F. Deleo, G. Didato, a Parente, C. Marras, M. G. Bruzzone, L. D’Incerti, R. Spreafico, and F. Villani, “Preoperative language lateralization in temporal lobe epilepsy (TLE) predicts peri-ictal, pre- and post-operative language performance: An fMRI study.,” NeuroImage. Clin., vol. 3, pp. 73–83, Jan. 2013.
26- A. Dimoka, “How to Conduct a Functional Magnetic Resonance (fMRI) Study in Social Science Research,” MIS Q., vol. 36, no. 3, pp. 811–840, 2012.
27- P. Matthews and P. Jezzard, “Functional magnetic resonance imaging,” J. Neurol. Neurosurg. Psychiatry, vol. 75, no. 1, pp. 6–12, Jan. 2004.
28- N. F. Ramsey, H. Hoogduin, and J. M. Jansma, “Functional MRI experiments: acquisition, analysis and interpretation of data,” Eur. Neuropsychopharmacol., vol. 12, no. 6, pp. 517–526, 2002.
29- E. Amaro and G. J. Barker, “Study design in fMRI: Basic principles,” Brain Cogn., vol. 60, no. 3, pp. 220–232, 2006.
30- C. C. Lee, H. A. Ward, F. W. Sharbrough, F. B. Meyer, W. R. Marsh, C. Raffel, E. L. So, G. D. Cascino, C. Shin, Y. Xu, S. J. Riederer, and C. R. Jack Jr, “Assessment of Functional MR Imaging in Neurosurgical Planning,” Am. J. Neuroradiol. , vol. 20, no. 8, pp. 1511–1519, Sep. 1999.
31- J. C. Gore, “Principles and practice of functional MRI of the human brain,” J. Clin. Invest., vol. 112, no. 1, pp. 4–9, Jul. 2003.
32- P. A. Bandettini, “Twenty years of functional MRI: The science and the stories,” Neuroimage, vol. 62, no. 2, pp. 575–588, 2012.
33- D. Chaimow, K. Uğurbil, and A. Shmuel, “Optimization of functional MRI for detection, decoding and high-resolution imaging of the response patterns of cortical columns,” Neuroimage, vol. 164, pp. 67–99, 2018.
34- J. J. Chen, “Functional MRI of brain physiology in aging and neurodegenerative diseases,” Neuroimage, 2018.
35- E. Bullmore, “The future of functional MRI in clinical medicine,” Neuroimage, vol. 62, no. 2, pp. 1267–1271, 2012.
36- T. E. Nichols, S. Das, S. B. Eickhoff, A. C. Evans, T. Glatard, M. Hanke, N. Kriegeskorte, M. P. Milham, R. A. Poldrack, J.-B. Poline, E. Proal, B. Thirion, D. C. Van Essen, T. White, and B. T. T. Yeo, “Best practices in data analysis and sharing in neuroimaging using MRI,” Nat. Neurosci., vol. 20, no. 3, pp. 299–303, Feb. 2017.
37- R. A. Poldrack, P. C. Fletcher, R. N. Henson, K. J. Worsley, M. Brett, and T. E. Nichols, “Guidelines for reporting an fMRI study,” Neuroimage, vol. 40, no. 2, pp. 409–414, Apr. 2008.
38- C. Caballero-Gaudes and R. C. Reynolds, “Methods for cleaning the BOLD fMRI signal,” Neuroimage, vol. 154, pp. 128–149, Jul. 2017.
39- R. R. Price, J. Allison, R. J. Massoth, G. D. Clarke, and D. J. Drost, “Practical aspects of functional MRI (NMR Task Group #8),” Med. Phys., vol. 29, no. 8, pp. 1892–1912, Aug. 2002.
40- M. Skup, “Longitudinal fMRI analysis: A review of methods,” Stat. Interface, vol. 3, no. 2, pp. 235–252, 2010.
41- E. H. Telzer, E. M. McCormick, S. Peters, D. Cosme, J. H. Pfeifer, and A. C. K. van Duijvenvoorde, “Methodological considerations for developmental longitudinal fMRI research,” Dev. Cogn. Neurosci., vol. 33, pp. 149–160, Oct. 2018.
42- M. H. Lee, C. D. Smyser, and J. S. Shimony, “Resting-state fMRI: a review of methods and clinical applications,” AJNR. Am. J. Neuroradiol., vol. 34, no. 10, pp. 1866–1872, Oct. 2013.
43- K. A. Smitha, K. Akhil Raja, K. M. Arun, P. G. Rajesh, B. Thomas, T. R. Kapilamoorthy, and C. Kesavadas, “Resting state fMRI: A review on methods in resting state connectivity analysis and resting state networks,” Neuroradiol. J., vol. 30, no. 4, pp. 305–317, Aug. 2017.
44- K. Li, L. Guo, J. Nie, G. Li, and T. Liu, “Review of methods for functional brain connectivity detection using fMRI,” Comput. Med. Imaging Graph., vol. 33, no. 2, pp. 131–139, Mar. 2009.
45- A. Bowring, C. Maumet, and T. Nichols, “Exploring the Impact of Analysis Software on Task fMRI Results,” bioRxiv, p. 285585, Jan. 2018.
46- J. M. Soares, R. Magalhães, P. S. Moreira, A. Sousa, E. Ganz, A. Sampaio, V. Alves, P. Marques, and N. Sousa, “A Hitchhiker’s Guide to Functional Magnetic Resonance Imaging ,” Frontiers in Neuroscience , vol. 10. p. 515, 2016.
47- S. A. H. Batouli, J. N. Trollor, W. Wen, and P. S. Sachdev, “The heritability of volumes of brain structures and its relationship to age: A review of twin and family studies,” Ageing Res. Rev., vol. 13, pp. 1–9, Jan. 2014.
48- B. Levine, E. Svoboda, J. F. Hay, G. Winocur, and M. Moscovitch, “Aging and autobiographical memory: Dissociating episodic from semantic retrieval.,” Psychology and Aging, vol. 17, no. 4. American Psychological Association, Levine, Brian: Rotman Research Inst, Baycrest Ctr for Geriatric Care, 3560 Bathurst Street, Toronto, ON, Canada, M6E 3A5, levine@psych.utoronto.ca, pp. 677–689, 2002.
49- L. P. Spear, “The adolescent brain and age-related behavioral manifestations,” Neurosci. Biobehav. Rev., vol. 24, no. 4, pp. 417–463, 2000.
50- E. R. Sowell, B. S. Peterson, P. M. Thompson, S. E. Welcome, A. L. Henkenius, and A. W. Toga, “Mapping cortical change across the human life span,” Nat Neurosci, vol. 6, no. 3, pp. 309–315, Mar. 2003.
51- E. D. O’Hare, L. H. Lu, S. M. Houston, S. Y. Bookheimer, and E. R. Sowell, “Neurodevelopmental Changes in Verbal Working Memory Load-Dependency: An fMRI Investigation,” Neuroimage, vol. 42, no. 4, pp. 1678–1685, Oct. 2008.
52- S. A. H. Batouli, P. S. Sachdev, W. Wen, M. J. Wright, D. Ames, and J. N. Trollor, “Heritability of brain volumes in older adults: the Older Australian Twins Study,” Neurobiol. Aging, vol. 35, no. 4, p. 937.e5-937.e18, Apr. 2014.
53- M. P. Kirschen, S. H. A. Chen, P. Schraedley-Desmond, and J. E. Desmond, “Load- and practice-dependent increases in cerebro-cerebellar activation in verbal working memory: an fMRI study,” Neuroimage, vol. 24, no. 2, pp. 462–472, 2005.
54- A. Kaiser, S. Haller, S. Schmitz, and C. Nitsch, “On sex/gender related similarities and differences in fMRI language research,” Brain Res. Rev., vol. 61, pp. 49–59, Jun. 2009.
55- S. A. H. Batouli and V. Saba, “Larger volume and a different activation of the brain in response to threat in military officers,” Basic Clin. Neurosci., vol. In Press., 2019.
56- K. Keller and V. Menon, “Gender differences in the functional and structural neuroanatomy of mathematical cognition,” Neuroimage, vol. 47, no. 1, pp. 342–352, Aug. 2009.
57- B. S. McEwen and T. A. Milner, “Understanding the broad influence of sex hormones and sex differences in the brain,” J. Neurosci. Res., vol. 95, no. 1–2, pp. 24–39, Jan. 2017.
58- L. Cahill, “Chapter 3 - Sex influences on brain and emotional memory: The burden of proof has shifted,” in Sex Differences in the Human Brain, their Underpinnings and Implications, vol. 186, I. B. T.-P. in B. R. Savic, Ed. Elsevier, 2010, pp. 29–40.
59- C.-H. Ko, J.-Y. Yen, C.-F. Yen, C.-S. Chen, W.-C. Lin, P.-W. Wang, and G.-C. Liu, “Brain activation deficit in increased-load working memory tasks among adults with ADHD using fMRI,” Eur. Arch. Psychiatry Clin. Neurosci., vol. 263, no. 7, pp. 561–573, 2013.
60- S. Zysset, K. Müller, C. Lehmann, A. I. . Thöne-Otto, and D. Y. von Cramon, “Retrieval of long and short lists from long term memory: a functional magnetic resonance imaging study with human subjects,” Neurosci. Lett., vol. 314, no. 1, pp. 1–4, 2001.
61- J. Rissman, A. Gazzaley, and M. D’Esposito, “The effect of non-visual working memory load on top-down modulation of visual processing,” Neuropsychologia, vol. 47, no. 7, pp. 1637–1646, Jun. 2009.
62- A. W. S. Leung and C. Alain, “Working memory load modulates the auditory ‘What’ and ‘Where’ neural networks,” Neuroimage, vol. 55, no. 3, pp. 1260–1269, 2011.
63- V. B. Van Hasselt, J. Milliones, and M. Hersen, “Behavioral Assessment of Drug Addiction: Strategies and Issues in Research and Treatment,” Int. J. Addict., vol. 16, no. 1, pp. 43–68, Jan. 1981.
64- A. Keihani, H. Ekhtiari, S. A. H. Batouli, A. Shahbabaie, N. Sadighi, M. Mirmohammad, and M. A. Oghabian, “Lower Gray Matter Density in the Anterior Cingulate Cortex and Putamen Can Be Traceable in Chronic Heroin Dependents After Over Three Months of Successful Abstinence,” Iran. J. Radiol., vol. 14, no. 3, p. e41858, 2017.
65- G. Winger, J. H. Woods, C. M. Galuska, and T. Wade-Galuska, “Behavioral perspectives on the neuroscience of drug addiction,” J. Exp. Anal. Behav., vol. 84, no. 3, pp. 667–681, Nov. 2005.
66- J. M. Kızılırmak, F. Rösler, and P. H. Khader, “Control processes during selective long-term memory retrieval,” Neuroimage, vol. 59, no. 2, pp. 1830–1841, 2012.
67- R. C. Oldfield, “The assessment and analysis of handedness: the Edinburgh inventory,” Neuropsychologia, vol. 9, no. 1. pp. 97–113, 1971.
68- R. M. Anderson, “Halstead-Reitan Neuropsychological Battery BT - Practitioner’s Guide to Clinical Neuropsychology,” R. M. Anderson, Ed. Boston, MA: Springer US, 1994, pp. 7–9.
69- J. L. Cuzzocreo, M. A. Yassa, G. Verduzco, N. A. Honeycutt, D. J. Scott, and S. S. Bassett, “Effect of handedness on fMRI activation in the medial temporal lobe during an auditory verbal memory task,” Hum. Brain Mapp., vol. 30, no. 4, pp. 1271–1278, Apr. 2009.
70- Q. Gao, J. Wang, C. Yu, and H. Chen, “Effect of handedness on brain activity patterns and effective connectivity network during the semantic task of Chinese characters,” Sci. Rep., vol. 5, p. 18262, Dec. 2015.
71- A. Flöel, B. Dräger, E.-B. Ringelstein, H. Henningsen, H. Lohmann, L. Bobe, M. Deppe, and S. Knecht, “Handedness and hemispheric language dominance in healthy humans,” Brain, vol. 123, no. 12, pp. 2512–2518, Dec. 2000.
72- M. A. Just, V. L. Cherkassky, A. Buchweitz, T. A. Keller, and T. M. Mitchell, “Identifying Autism from Neural Representations of Social Interactions: Neurocognitive Markers of Autism,” PLoS One, vol. 9, no. 12, p. e113879, Dec. 2014.
73- G. Chanel, S. Pichon, L. Conty, S. Berthoz, C. Chevallier, and J. Grèzes, “Classification of autistic individuals and controls using cross-task characterization of fMRI activity,” NeuroImage Clin., vol. 10, pp. 78–88, 2016.
74- S. M. Daselaar, S. E. Prince, and R. Cabeza, “When less means more: deactivations during encoding that predict subsequent memory,” Neuroimage, vol. 23, no. 3, pp. 921–927, 2004.
75- J. M. Kizilirmak, F. Rösler, and P. H. Khader, “Control processes during selective long-term memory retrieval,” Neuroimage, vol. 59, no. 2, pp. 1830–1841, 2012.
76- M. Toepper, H. J. Markowitsch, H. Gebhardt, T. Beblo, C. Thomas, B. Gallhofer, M. Driessen, and G. Sammer, “Hippocampal involvement in working memory encoding of changing locations: An fMRI study,” Brain Res., vol. 1354, pp. 91–99, Oct. 2010.
77- M. F. Folstein, S. E. Folstein, and P. R. McHugh, “‘Mini-mental state’. A practical method for grading the cognitive state of patients for the clinician.,” J. Psychiatr. Res., vol. 12, no. 3, pp. 189–198, 1975.
78- S. A. H. Batouli, P. S. Sachdev, W. Wen, M. J. Wright, C. Suo, D. Ames, and J. N. Trollor, “The heritability of brain metabolites on proton magnetic resonance spectroscopy in older individuals,” Neuroimage, vol. 62, no. 1, pp. 281–289, Aug. 2012.
79- S. Nikolova, R. Bartha, A. G. Parrent, D. A. Steven, D. Diosy, and J. G. Burneo, “Functional MRI of neuronal activation in epilepsy patients with malformations of cortical development,” Epilepsy Res., vol. 116, pp. 1–7, 2015.
80- S.-L. Lim, S. Padmala, and L. Pessoa, “Affective learning modulates spatial competition during low-load attentional conditions,” Neuropsychologia, vol. 46, no. 5, pp. 1267–1278, Apr. 2008.
81- D. Fegen, B. R. Buchsbaum, and M. D’Esposito, “The effect of rehearsal rate and memory load on verbal working memory,” Neuroimage, vol. 105, pp. 120–131, 2015.
82- S. Huang, L. J. Seidman, S. Rossi, and J. Ahveninen, “Distinct cortical networks activated by auditory attention and working memory load,” Neuroimage, vol. 83, p. 10.1016/j.neuroimage.2013.07.074, Dec. 2013.
83- K. Murphy and H. Garavan, “An empirical investigation into the number of subjects required for an event-related fMRI study,” Neuroimage, vol. 22, no. 2, pp. 879–885, 2004.
84- K. J. Friston, A. Holmes, J.-B. Poline, C. J. Price, and C. D. Frith, “Detecting Activations in PET and fMRI: Levels of Inference and Power,” Neuroimage, vol. 4, no. 3, pp. 223–235, 1996.
85- J. E. Desmond and G. H. Glover, “Estimating sample size in functional MRI (fMRI) neuroimaging studies: Statistical power analyses,” J. Neurosci. Methods, vol. 118, no. 2, pp. 115–128, 2002.
86- J. A. Mumford and T. E. Nichols, “Power calculation for group fMRI studies accounting for arbitrary design and temporal autocorrelation,” Neuroimage, vol. 39, no. 1, pp. 261–268, Jan. 2008.
87- J. A. Mumford, “A power calculation guide for fMRI studies,” Soc. Cogn. Affect. Neurosci., vol. 7, no. 6, pp. 738–742, Aug. 2012.
88- K. E. Joyce and S. Hayasaka, “Development of PowerMap: a software package for statistical power calculation in neuroimaging studies,” Neuroinformatics, vol. 10, no. 4, pp. 351–365, Oct. 2012.
89- H.-Y. Kim, “Statistical notes for clinical researchers: effect size,” Restor. Dent. Endod., vol. 40, no. 4, pp. 328–331, Nov. 2015.
90- H. Magen, T.-A. Emmanouil, S. A. McMains, S. Kastner, and A. Treisman, “Attentional demands predict short-term memory load response in posterior parietal cortex,” Neuropsychologia, vol. 47, no. 8–9, pp. 1790–1798, Jul. 2009.
91- D. Pinal, M. Zurrón, and F. Díaz, “Effects of load and maintenance duration on the time course of information encoding and retrieval in working memory: from perceptual analysis to post-categorization processes ,” Frontiers in Human Neuroscience , vol. 8. p. 165, 2014.
92- Y. Koush, D.-E. Meskaldji, S. Pichon, G. Rey, S. W. Rieger, D. E. J. Linden, D. Van De Ville, P. Vuilleumier, and F. Scharnowski, “Learning Control Over Emotion Networks Through Connectivity-Based Neurofeedback,” Cereb. Cortex, vol. 27, no. 2, pp. 1193–1202, Feb. 2017.
93- N. Axmacher, S. Haupt, M. X. Cohen, C. E. Elger, and J. Fell, “Interference of working memory load with long-term memory formation,” Eur. J. Neurosci., vol. 29, no. 7, pp. 1501–1513, Mar. 2009.
94- T. S. Woodward, T. A. Cairo, C. C. Ruff, Y. Takane, M. A. Hunter, and E. T. C. Ngan, “Functional connectivity reveals load dependent neural systems underlying encoding and maintenance in verbal working memory,” Neuroscience, vol. 139, no. 1, pp. 317–325, 2006.
95- B. Maus and G. J. P. van Breukelen, “Optimal Design for Functional Magnetic Resonance Imaging Experiments,” Z. Psychol., vol. 221, no. 3, pp. 174–189, Jan. 2013.
96- T. A. Cairo, P. F. Liddle, T. S. Woodward, and E. T. C. Ngan, “The influence of working memory load on phase specific patterns of cortical activity,” Cogn. Brain Res., vol. 21, no. 3, pp. 377–387, 2004.
97- Y. Tie, R. O. Suarez, S. Whalen, A. Radmanesh, I. H. Norton, and A. J. Golby, “Comparison of blocked and event-related fMRI designs for pre-surgical language mapping.,” Neuroimage, vol. 47 Suppl 2, pp. T107-15, Aug. 2009.
98- K. J. Friston, A. P. Holmes, C. J. Price, C. Büchel, and K. J. Worsley, “Multisubject fMRI Studies and Conjunction Analyses,” Neuroimage, vol. 10, no. 4, pp. 385–396, 1999.
99- S. A. Huettel, “Event-related fMRI in cognition,” Neuroimage, vol. 62, no. 2, pp. 1152–1156, Aug. 2012.
100- T. T. Liu, “The development of event-related fMRI designs,” Neuroimage, vol. 62, no. 2, pp. 1157–1162, Aug. 2012.
101- T. T. Liu, L. R. Frank, E. C. Wong, and R. B. Buxton, “Detection Power, Estimation Efficiency, and Predictability in Event-Related fMRI,” Neuroimage, vol. 13, no. 4, pp. 759–773, 2001.
102- M. Toepper, H. Gebhardt, E. Bauer, A. Haberkamp, T. Beblo, B. Gallhofer, M. Driessen, and G. Sammer, “The impact of age on load-related dorsolateral prefrontal cortex activation ,” Frontiers in Aging Neuroscience , vol. 6. p. 9, 2014.
103- Q. Miao, G. Zhang, W. Yan, and B. Liu, “Investigating the Brain Neural Mechanism when Signature Objects were Masked during a Scene Categorization Task using Functional MRI,” Neuroscience, vol. 388, pp. 248–262, 2018.
104- K. Diers, F. Weber, B. Brocke, A. Strobel, and S. Schönfeld, “Instructions matter: a comparison of baseline conditions for cognitive emotion regulation paradigms ,” Frontiers in Psychology , vol. 5. p. 347, 2014.
105- M. W. L. Chee, V. Venkatraman, C. Westphal, and S. C. Siong, “Comparison of block and event-related fMRI designs in evaluating the word-frequency effect,” Hum. Brain Mapp., vol. 18, no. 3, pp. 186–193, Mar. 2003.
106- C. E. Stark and L. R. Squire, “When zero is not zero: the problem of ambiguous baseline conditions in fMRI,” Proc. Natl. Acad. Sci. U. S. A., vol. 98, no. 22, pp. 12760–12766, Oct. 2001.
107- M. Intaitė, J. V. Duarte, and M. Castelo-Branco, “Working memory load influences perceptual ambiguity by competing for fronto-parietal attentional resources,” Brain Res., vol. 1650, pp. 142–151, 2016.
108- M. Sobczak-Edmans, T. H. B. Ng, Y. C. Chan, E. Chew, K. H. Chuang, and S. H. A. Chen, “Temporal dynamics of visual working memory,” Neuroimage, vol. 124, pp. 1021–1030, 2016.
109- S. Steinvorth, S. Corkin, and E. Halgren, “Ecphory of Autobiographical Memories: an fMRI Study on Recent and Remote Memory Retrieval,” Neuroimage, vol. 30, no. 1, pp. 285–298, Mar. 2006.
110- M. Ullsperger and D. Y. von Cramon, “Error Monitoring Using External Feedback: Specific Roles of the Habenular Complex, the Reward System, and the Cingulate Motor Area Revealed by Functional Magnetic Resonance Imaging,” J. Neurosci., vol. 23, no. 10, p. 4308 LP-4314, May 2003.
111- C. Silvestre, P. Figueiredo, and P. Rosa, “On the distinguishability of HRF models in fMRI,” in 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology, 2010, pp. 5677–5680.
112- D. A. Handwerker, J. M. Ollinger, and M. D’Esposito, “Variation of BOLD hemodynamic responses across subjects and brain regions and their effects on statistical analyses,” Neuroimage, vol. 21, no. 4, pp. 1639–1651, 2004.
113- G. K. Aguirre, E. Zarahn, and M. D’Esposito, “The Variability of Human, BOLD Hemodynamic Responses,” Neuroimage, vol. 8, no. 4, pp. 360–369, 1998.
114- E. R. Cohen, K. Ugurbil, and S.-G. Kim, “Effect of Basal Conditions on the Magnitude and Dynamics of the Blood Oxygenation Level-Dependent fMRI Response,” J. Cereb. Blood Flow Metab., vol. 22, no. 9, pp. 1042–1053, Sep. 2002.
115- T. T. Liu, Y. Behzadi, K. Restom, K. Uludag, K. Lu, G. T. Buracas, D. J. Dubowitz, and R. B. Buxton, “Caffeine alters the temporal dynamics of the visual BOLD response,” Neuroimage, vol. 23, no. 4, pp. 1402–1413, 2004.
116- M. D’Esposito, L. Y. Deouell, and A. Gazzaley, “Alterations in the BOLD fMRI signal with ageing and disease: a challenge for neuroimaging,” Nat. Rev. Neurosci., vol. 4, p. 863, Nov. 2003.
117- V. D. Calhoun and T. Adali, “Unmixing fMRI with independent component analysis,” IEEE Eng. Med. Biol. Mag., vol. 25, no. 2, pp. 79–90, 2006.
118- M. Toepper, H. J. Markowitsch, H. Gebhardt, T. Beblo, C. Thomas, B. Gallhofer, M. Driessen, and G. Sammer, “Hippocampal involvement in working memory encoding of changing locations: an fMRI study.,” Brain Res., vol. 1354, pp. 91–9, 2010.
119- T. A. Kelley and N. Lavie, “Working Memory Load Modulates Distractor Competition in Primary Visual Cortex,” Cereb. Cortex (New York, NY), vol. 21, no. 3, pp. 659–665, Mar. 2011.
120- C. H. Meyer, B. S. Hu, D. G. Nishimura, and A. Macovski, “Fast Spiral Coronary Artery Imaging,” Magn. Reson. Med., vol. 28, no. 2, pp. 202–213, Oct. 1992.
121- Y. Ye, Y. Zhuo, R. Xue, and X. J. Zhou, “BOLD fMRI using a modified HASTE sequence,” Neuroimage, vol. 49, no. 1, pp. 457–466, Jan. 2010.
122- B. A. Poser and D. G. Norris, “Fast spin echo sequences for BOLD functional MRI,” MAGMA, vol. 20, no. 1, pp. 11–17, Feb. 2007.
123- E. Yacoub, P.-F. Van De Moortele, A. Shmuel, and K. Uğurbil, “Signal and noise characteristics of Hahn SE and GE BOLD fMRI at 7 T in humans,” Neuroimage, vol. 24, no. 3, pp. 738–750, 2005.
124- G. H. Glover and S. Lai, “Self-navigated spiral fMRI: Interleaved versus single-shot,” Magn. Reson. Med., vol. 39, no. 3, pp. 361–368, Dec. 1998.
125- N. Weiskopf, C. Hutton, O. Josephs, and R. Deichmann, “Optimal EPI parameters for reduction of susceptibility-induced BOLD sensitivity losses: A whole-brain analysis at 3 T and 1.5 T,” Neuroimage, vol. 33, no. 2, pp. 493–504, 2006.
126- J. Gonzalez-Castillo, V. Roopchansingh, P. A. Bandettini, and J. Bodurka, “Physiological noise effects on the flip angle selection in BOLD fMRI,” Neuroimage, vol. 54, no. 4, pp. 2764–2778, Feb. 2011.
127- C. Preibisch, T. Wallenhorst, R. Heidemann, F. E. Zanella, and H. Lanfermann, “Comparison of parallel acquisition techniques generalized autocalibrating partially parallel acquisitions (GRAPPA) and modified sensitivity encoding (mSENSE) in functional MRI (fMRI) at 3T,” J. Magn. Reson. Imaging, vol. 27, no. 3, pp. 590–598, Mar. 2008.
128- P. van Gelderen, J. H. Duyn, N. F. Ramsey, G. Liu, and C. T. W. Moonen, “The PRESTO technique for fMRI,” Neuroimage, vol. 62, no. 2, pp. 676–681, Aug. 2012.
129- G. H. Glover, T.-Q. Li, and D. Ress, “Image-based method for retrospective correction of physiological motion effects in fMRI: RETROICOR,” Magn. Reson. Med., vol. 44, no. 1, pp. 162–167, Jul. 2000.
130- H.-C. Leung, D. Seelig, and J. C Gore, The effect of memory load on cortical activity in the spatial working memory circuit, vol. 4. 2005.
131- A. Rosset, L. Spadola, and O. Ratib, “OsiriX: an open-source software for navigating in multidimensional DICOM images,” J. Digit. Imaging, vol. 17, no. 3, pp. 205–216, Sep. 2004.
132- T. Stöcker, F. Schneider, M. Klein, U. Habel, T. Kellermann, K. Zilles, and N. J. Shah, “Automated quality assurance routines for fMRI data applied to a multicenter study,” Hum. Brain Mapp., vol. 25, no. 2, pp. 237–246, Jun. 2005.
133- A. G. Christodoulou, T. E. Bauer, K. A. Kiehl, S. W. Feldstein Ewing, A. D. Bryan, and V. D. Calhoun, “A quality control method for detecting and suppressing uncorrected residual motion in fMRI studies,” Magn. Reson. Imaging, vol. 31, no. 5, pp. 707–717, Jun. 2013.
134- J. D. Power, “A simple but useful way to assess fMRI scan qualities,” Neuroimage, vol. 154, pp. 150–158, Jul. 2017.
135- R. Sladky, K. J. Friston, J. Tröstl, R. Cunnington, E. Moser, and C. Windischberger, “Slice-timing effects and their correction in functional MRI,” Neuroimage, vol. 58, no. 2, pp. 588–594, Sep. 2011.
136- S. M. Smith, “Fast robust automated brain extraction,” Hum. Brain Mapp., vol. 17, no. 3, pp. 143–155, Sep. 2002.
137- D. Dima, J. Jogia, and S. Frangou, “Dynamic causal modeling of load-dependent modulation of effective connectivity within the verbal working memory network,” Hum. Brain Mapp., vol. 35, no. 7, pp. 3025–3035, Oct. 2013.
138- V. Zotev, H. Yuan, R. Phillips, and J. Bodurka, “EEG-assisted retrospective motion correction for fMRI: E-REMCOR,” Neuroimage, vol. 63, no. 2, pp. 698–712, 2012.
139- M. Zaitsev, B. Akin, P. LeVan, and B. R. Knowles, “Prospective motion correction in functional MRI,” Neuroimage, vol. 154, pp. 33–42, Jul. 2017.
140- R. Yakupov, J. Lei, M. B. Hoffmann, and O. Speck, “False fMRI activation after motion correction,” Hum. Brain Mapp., vol. 38, no. 9, pp. 4497–4510, Sep. 2017.
141- M. Stollstorff, J. Foss-Feig, E. H. Cook, M. A. Stein, W. D. Gaillard, and C. J. Vaidya, “Neural response to working memory load varies by dopamine transporter genotype in children,” Neuroimage, vol. 53, no. 3, pp. 970–977, Nov. 2010.
142- P. K. Bhattacharyya and M. J. Lowe, “Cardiac-induced physiologic noise in tissue is a direct observation of cardiac-induced fluctuations,” Magn. Reson. Imaging, vol. 22, no. 1, pp. 9–13, 2004.
143- J. R. Brosch, T. M. Talavage, J. L. Ulmer, and J. A. Nyenhuis, “Simulation of human respiration in fMRI with a mechanical model,” IEEE Trans. Biomed. Eng., vol. 49, no. 7, pp. 700–707, 2002.
144- J. C. W. Brooks, O. K. Faull, K. T. S. Pattinson, and M. Jenkinson, “Physiological noise in brainstem FMRI,” Front. Hum. Neurosci., vol. 7, p. 623, Oct. 2013.
145- M. Behroozi, M. R. Daliri, and H. Boyaci, “Statistical Analysis Methods for the fMRI Data TT -,” BCN, vol. 2, no. 4. pp. 67–74, 2011.
146- K. J. Friston, A. P. Holmes, J.-B. Poline, P. J. Grasby, S. C. R. Williams, R. S. J. Frackowiak, and R. Turner, “Analysis of fMRI Time-Series Revisited,” Neuroimage, vol. 2, no. 1, pp. 45–53, 1995.
147- M. M. Monti, “Statistical Analysis of fMRI Time-Series: A Critical Review of the GLM Approach,” Front. Hum. Neurosci., vol. 5, p. 28, Mar. 2011.
148- F. D. Bowman, Y. Guo, and G. Derado, “Statistical approaches to functional neuroimaging data,” Neuroimaging Clin. N. Am., vol. 17, no. 4, p. 441–viii, Nov. 2007.
149- D. E. J. Linden, R. A. Bittner, L. Muckli, J. A. Waltz, N. Kriegeskorte, R. Goebel, W. Singer, and M. H. J. Munk, “Cortical capacity constraints for visual working memory: dissociation of fMRI load effects in a fronto-parietal network,” Neuroimage, vol. 20, no. 3, pp. 1518–1530, 2003.
150- N. Tzourio-Mazoyer, B. Landeau, D. Papathanassiou, F. Crivello, O. Etard, N. Delcroix, B. Mazoyer, and M. Joliot, “Automated Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject Brain,” Neuroimage, vol. 15, no. 1, pp. 273–289, 2002.
151- C. R. Genovese, N. A. Lazar, and T. Nichols, “Thresholding of Statistical Maps in Functional Neuroimaging Using the False Discovery Rate,” Neuroimage, vol. 15, no. 4, pp. 870–878, 2002.
152- R. G. and F. D. S. Luigi Trojano, Dario Grossi, David E.J. Linden, Elia Formisano, Hans Hacker, Friedhelm E. Zanella, “Matching Two Imagined Clocks: the Functional Anatomy of Spatial Analysis in the Absence of Visual Stimulation,” Cereb. Cortex, vol. 10, no. 7, p. 727, Jul. 2000.
153- L. Muckli, N. Kriegeskorte, H. Lanfermann, F. E. Zanella, W. Singer, and R. Goebel, “Apparent Motion: Event-Related Functional Magnetic Resonance Imaging of Perceptual Switches and States,” J. Neurosci., vol. 22, no. 9, p. RC219 LP-RC219, May 2002.
154- R. A. Poldrack, “The role of fMRI in Cognitive Neuroscience: where do we stand?,” Curr. Opin. Neurobiol., vol. 18, no. 2, pp. 223–227, 2008.
155- R. L. Gould, R. G. Brown, A. M. Owen, D. H. ffytche, and R. J. Howard, “FMRI BOLD response to increasing task difficulty during successful paired associates learning,” Neuroimage, vol. 20, no. 2, pp. 1006–1019, 2003.
156- J. J. Todd and R. Marois, “Capacity limit of visual short-term memory in human posterior parietal cortex,” Nature, vol. 428, p. 751, Apr. 2004.
157- P. Mazaika, “Percent Signal Change for fMRI calculations,” 2009.
158- R. A. Poldrack, “Region of interest analysis for fMRI,” Soc. Cogn. Affect. Neurosci., vol. 2, no. 1, pp. 67–70, Mar. 2007.
159- R. A. Klein, K. A. Ratliff, M. Vianello, R. B. Adams, Š. Bahník, M. J. Bernstein, K. Bocian, M. J. Brandt, B. Brooks, C. C. Brumbaugh, Z. Cemalcilar, J. Chandler, W. Cheong, W. E. Davis, T. Devos, M. Eisner, N. Frankowska, D. Furrow, E. M. Galliani, F. Hasselman, J. A. Hicks, J. F. Hovermale, S. J. Hunt, J. R. Huntsinger, H. IJzerman, M.-S. John, J. A. Joy-Gaba, H. Barry Kappes, L. E. Krueger, J. Kurtz, C. A. Levitan, R. K. Mallett, W. L. Morris, A. J. Nelson, J. A. Nier, G. Packard, R. Pilati, A. M. Rutchick, K. Schmidt, J. L. Skorinko, R. Smith, T. G. Steiner, J. Storbeck, L. M. Van Swol, D. Thompson, A. E. van ‘t Veer, L. Ann Vaughn, M. Vranka, A. L. Wichman, J. A. Woodzicka, and B. A. Nosek, “Investigating Variation in Replicability,” Soc. Psychol. (Gott)., vol. 45, no. 3, pp. 142–152, Jan. 2014.
160- J. Carp, “The secret lives of experiments: Methods reporting in the fMRI literature,” Neuroimage, vol. 63, no. 1, pp. 289–300, 2012.
161- C. Maumet, T. Auer, A. Bowring, G. Chen, S. Das, G. Flandin, S. Ghosh, T. Glatard, K. J. Gorgolewski, K. G. Helmer, M. Jenkinson, D. B. Keator, B. N. Nichols, J.-B. Poline, R. Reynolds, V. Sochat, J. Turner, and T. E. Nichols, “Sharing brain mapping statistical results with the neuroimaging data model,” Sci. data, vol. 3, p. 160102, Dec. 2016.
162- J. P. Roiser, D. E. Linden, M. L. Gorno-Tempinin, R. J. Moran, B. C. Dickerson, and S. T. Grafton, “Minimum statistical standards for submissions to Neuroimage: Clinical,” NeuroImage. Clin., vol. 12, pp. 1045–1047, Nov. 2016.
163- D. A. Orringer, D. R. Vago, and A. J. Golby, “Clinical applications and future directions of functional MRI,” Semin. Neurol., vol. 32, no. 4, pp. 466–475, Sep. 2012.
164- R. A. Poldrack, “The future of fMRI in cognitive neuroscience,” Neuroimage, vol. 62, no. 2, pp. 1216–1220, Aug. 2012.
165- M. A. Rocca, “Present and future of fMRI in multiple sclerosis AU - Filippi, Massimo,” Expert Rev. Neurother., vol. 13, no. sup2, pp. 27–31, Dec. 2013.
Files
IssueVol 7 No 1 (2020) QRcode
SectionLiterature (Narrative) Review(s)
DOI https://doi.org/10.18502/fbt.v7i1.2725
Keywords
Functional Magnetic Resonance Imaging Experiment Design Task-Based

Rights and permissions
Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
How to Cite
1.
Batouli SAH, Sisakhti M. Some Points to Consider in a Task-Based fMRI Study: A Guideline for Beginners. Frontiers Biomed Technol. 2020;7(1):52-73.