HST.583LAB 3: Improving fMRI signal detection usingphysiological dataOctober 17, 2001IntroductionThis Lab examines two ways that physiological data can be used to improve fMRIsignal detection.Cardiac GatingPart I of this Lab focuses on cardiac gating. This technique uses a subject's EKGrecorded during an experiment to improve fMRI signal detection. Cardiac gating is usedto overcome a technical difficulty associated with functionally imaging brainstemstructures. This difficulty arises because there is considerable cardiac-related, pulsatilebrainstem motion. Cardiac gating avoids this problem by (1) synchronizing imageacquisitions to the subject heart beat, then (2) correcting image signal strength to accountfor the variability in interimage interval (TR) that results from fluctuations in heart rate(Guimaraes et. al., 1998).In this Lab, the effects of cardiac gating are examined for structures in theauditory system. Sounds are processed extensively within auditory brainstem structures,and cardiac gating is important for investigating this processing. The Lab will focus ontwo particular auditory structures. One is the inferior colliculus. This brainstem structureis a major site of converging projections from both lower and higher brain centers. Thesecond structure is Heschl's gyrus, the site of primary auditory cortex.Clustered Volume Acquisition (CVA)Part II of this Lab examines a technique for minimizing the effects of scanneracoustic noise on auditory activation. This technique is called clustered volumeacquisition (CVA). Unlike cardiac gating, CVA does not use physiological data recordedduring each experiment to improve signal detection. However, the technique is baseddirectly on physiological data, specifically general information concerning the temporalcharacteristics of fMRI responses (i.e., response latency, duration).There are two main types of acoustic noise in the imaging environment. One is anon-going noise produced by the pumping of coolant to the magnet. The second, moreintense noise is intermittent. It is produced by the scanner gradient coils each time animage is acquired. The noise can pose difficulties for studies using sound stimuli by (1)masking the stimuli, and (2) inducing brain activity that is not related to the stimuli (thisnoise-related brain activity acts to suppress the fMRI signal changes produced by theintended sound stimuli).CVA provides a way to reduce the effects of the most problematic noise, namelythe noise produced by the gradient coils. CVA involves imaging a volume of slices in a“cluster” and leaving a quiet interval between clusters (Edmister et. al., 1999; Hall et. al.,1999). With this paradigm, the masking effects of the gradient noise can be avoided bypresenting sound stimuli during the quiet interval. In addition, the suppressive effect ofthe gradient noise on auditory activation can be avoided by (1) making the duration of theimage cluster shorter than the onset time of the fMRI response to the first image in thecluster, and (2) making the time between clusters (TR) longer than the fMRI response toa cluster.The benefits of CVA for detecting activation in auditory cortex were illustrated inlecture. In this Lab, you will examine how these benefits can be extended to subcorticalstructures by combining CVA with cardiac gating. When CVA is used with a long TR(e.g., ≥ 8 sec), image signals are sampled far less frequently than in most fMRI studies.The implications of this lower temporal resolution for experimental design will also beexamined in this Lab.Lab OverviewThe organization of the data for this lab is as follows:Part I: Cardiac Gating (data are in the directory Lab3.1)Part II: Clustered Volume Acquisition (CVA)(a) Combining CVA and cardiac gating (data are in the directory Lab3.2a)(b) CVA and temporal sampling (data are in the directory Lab3.2b).The software tools for this lab are programs that run from the command line in theAthena environment:standard_deviation - generates maps of the standard deviation in image signalover time for every voxelgating_correction – corrects cardiac-gated data for variations in image signal dueto fluctuations in heart ratexds - package for visualizing anatomical and functional images, statistical maps,MR signal vs. time, etc.Each tool is described in detail in the Appendix – “Software Tools” at the end of thishandout.Guidelines for Laboratory ReportYour laboratory report should contain answers to the questions specified below.Do not repeat the lab instructions and avoid lengthy introductions. Your report should notexceed 4 pages. Conclude your report with a few sentences summarizing what youlearned in the lab.Part I: Cardiac GatingThis part of the Lab is designed to give you a physical feeling for data acquiredwith and without cardiac gating. Many of the analyses you will perform parallel those ofGuimaraes et al. (1998), so you may find their paper useful in completing this part of theLab.Specific Instructions:To get started, typeattach hst.583cp -r /afs/athena.mit.edu/course/other/hst.583/lab_data/lab3 .Directory Lab3.1 contains two sets of functional images (A.bshort and B.bshort).Both were acquired using a standard fMRI block paradigm, i.e. a stimulus (orchestralmusic) was repeatedly turned on for 30 sec and off for 30 sec. For both sets of data, asingle slice was imaged which passed through the inferior colliculi and Heschl's gyri(Figure 1). One data set was acquired using a fixed TR (= 2 sec). The other data set wasacquired in the same experiment using cardiac gating. In this case, the subject'selectrocardiogram was measured and used to trigger the scanner. Images were acquiredevery other heart beat (Figure 2) so that the TR would be approximately the same as forthe "fixed TR" data set (i.e., ~2 sec; Note that a typical heart rate is ~60 beats/ min = 1beat/sec). Directory Lab3.1 also contains files A.para and B.para with information onthe experimental paradigm. Specifically, they contain a code for each successivefunctional image in *.bshort. The code indicates whether an image was acquired duringthe "stimulus on" condition (1) or the "stimulus off" condition (-1).Figure 1: T1-weighted anatomical Figure 2: Timing of imageimage of the functionally imaged slice. acquisitions relative to EKG during cardiac gating.The files LeftIC_lowres.ovl, RightIC_lowres.ovl, LeftHG_lowres.ovl andRightHG_lowres.ovl in Lab3.1 contain the coordinates