Does higher sampling rate (multiband + SENSE) improve group statistics - An example from social neuroscience block design at 3T

Multiband (MB) or Simultaneous multi-slice (SMS) acquisition schemes allow the acquisition of MRI signals from more than one spatial coordinate at a time. Commercial availability has brought this technique within the reach of many neuroscientists and psychologists. Most early evaluation of the performance of MB acquisition employed resting state fMRI or the most basic tasks. In this study, we tested whether the advantages of using MB acquisition schemes generalize to group analyses using a cognitive task more representative of typical cognitive neuroscience applications. Twenty-three subjects were scanned on a Philips 3 ​T scanner using five sequences, up to eight-fold acceleration with MB-factors 1 to 4, SENSE factors up to 2 and corresponding TRs of 2.45s down to 0.63s, while they viewed (i) movie blocks showing complex actions with hand object interactions and (ii) control movie blocks without hand object interaction. Data were processed using a widely used analysis pipeline implemented in SPM12 including the unified segmentation and canonical HRF modelling. Using random effects group-level, voxel-wise analysis we found that all sequences were able to detect the basic action observation network known to be recruited by our task. The highest t-values were found for sequences with MB4 acceleration. For the MB1 sequence, a 50% bigger voxel volume was needed to reach comparable t-statistics. The group-level t-values for resting state networks (RSNs) were also highest for MB4 sequences. Here the MB1 sequence with larger voxel size did not perform comparable to the MB4 sequence. Altogether, we can thus recommend the use of MB4 (and SENSE 1.5 or 2) on a Philips scanner when aiming to perform group-level analyses using cognitive block design fMRI tasks and voxel sizes in the range of cortical thickness (e.g. 2.7 ​mm isotropic). While results will not be dramatically changed by the use of multiband, our results suggest that MB will bring a moderate but significant benefit

Impacts of Simultaneous Multislice Acquisition on Sensitivity and Specificity in fMRI

Simultaneous multislice (SMS) imaging can be used to decrease the time between acquisition of fMRI volumes, which can increase sensitivity by facilitating the removal of higher-frequency artifacts and boosting effective sample size. The technique requires an additional processing step in which the slices are separated, or unaliased, to recover the whole brain volume. However, this may result in signal “leakage” between aliased locations, i.e., slice “leakage,” and lead to spurious activation (decreased specificity). SMS can also lead to noise amplification, which can reduce the benefits of decreased repetition time. In this study, we evaluate the original slice-GRAPPA (no leak block) reconstruction algorithmand acceleration factor (AF = 8) used in the fMRI data in the young adult Human Connectome Project (HCP). We also evaluate split slice-GRAPPA (leak block), which can reduce slice leakage. We use simulations to disentangle higher test statistics into true positives (sensitivity) and false positives (decreased specificity). Slice leakage was greatly decreased by split slice-GRAPPA. Noise amplification was decreased by using moderate acceleration factors (AF = 4). We examined slice leakage in unprocessed fMRI motor task data from the HCP. When data were smoothed, we found evidence of slice leakage in some, but not all, subjects. We also found evidence of SMS noise amplification in unprocessed task and processed resting-state HCP data

Temporal Signal-to-Noise Changes in Combined Multislice- and In-Plane-Accelerated Echo-Planar Imaging with a 20- and 64-Channel Coil

Echo-planar imaging (EPI) is the most common method of functional MRI for acquiring the blood oxygenation level-dependent (BOLD) contrast, allowing the acquisition of an entire brain volume within seconds. However, because imaging protocols are limited by hardware (e.g., fast gradient switching), researchers must compromise between spatial resolution, temporal resolution, or whole-brain coverage. Earlier attempts to circumvent this problem included developing protocols in which slices of a volume were acquired faster (i.e., in-plane acceleration (S)) or simultaneously (i.e., multislice acceleration (M)). However, applying acceleration methods can lead to a reduction in the temporal signal-to-noise ratio (tSNR): a critical measure of signal stability over time. Using a 20- and 64-channel receiver coil, we show that enabling S-acceleration consistently yielded a substantial decrease in tSNR, regardless of the receiver coil, whereas M-acceleration yielded less pronounced tSNR decrease. Moreover, tSNR losses tended to occur in temporal, insular, and medial brain regions and were more noticeable with the 20-channel coil, while with the 64-channel coil, the tSNR in lateral frontoparietal regions remained relatively stable up to six-fold M-acceleration producing comparable tSNR to that of no acceleration. Such methodological explorations can guide researchers and clinicians in optimizing imaging protocols depending on the brain regions under investigation

An empirical investigation of the benefit of increasing the temporal resolution of task-evoked fMRI data with multi-band imaging

Objective There is a tendency for reducing TR in MRI experiments with multi-band imaging. We empirically investigate its benefit for the group-level statistical outcome in task-evoked fMRI. Methods Three visual fMRI data sets were collected from 17 healthy adult participants. Multi-band acquisition helped vary the TR (2000/1000/410 ms, respectively). Because these data sets capture different temporal aspects of the haemodynamic response (HRF), we tested several HRF models. We computed a composite descriptive statistic, H, from β’s of each first-level model fit and carried it to the group-level analysis. The number of activated voxels and the t value of the group-level analysis as well as a goodness-of-fit measure were used as surrogate markers of data quality for comparison. Results Increasing the temporal sampling rate did not provide a universal improvement in the group-level statistical outcome. Rather, both the voxel-wise and ROI-averaged group-level results varied widely with anatomical location, choice of HRF and the setting of the TR. Correspondingly, the goodness-of-fit of HRFs became worse with increasing the sampling frequency. Conclusion Rather than universally increasing the temporal sampling rate in cognitive fMRI experiments, these results advocate the performance of a pilot study for the specific ROIs of interest to identify the appropriate temporal sampling rate for the acquisition and the correspondingly suitable HRF for the analysis of the data

fMRI protocol optimization for simultaneously studying small subcortical and cortical areas at 7 ​T

Most fundamental cognitive processes rely on brain networks that include both cortical and subcortical structures. Studying such networks using functional magnetic resonance imaging (fMRI) requires a data acquisition protocol that provides blood-oxygenation-level dependent (BOLD) sensitivity across the entire brain. However, when using standard single echo, echo planar imaging protocols, researchers face a tradeoff between BOLD-sensitivity in cortex and in subcortical areas. Multi echo protocols avoid this tradeoff and can be used to optimize BOLD-sensitivity across the entire brain, at the cost of an increased repetition time. Here, we empirically compare the BOLD-sensitivity of a single echo protocol to a multi echo protocol. Both protocols were designed to meet the specific requirements for studying small, iron rich subcortical structures (including a relatively high spatial resolution and short echo times), while retaining coverage and BOLD-sensitivity in cortical areas. The results indicate that both sequences lead to similar BOLD-sensitivity across the brain at 7 ​T

Safety and data quality of EEG recorded simultaneously with multi-band fMRI

Simultaneously recorded electroencephalography and functional magnetic resonance imaging (EEG-fMRI) is highly informative yet technically challenging. Until recently, there has been little information about EEG data quality and safety when used with newer multi-band (MB) fMRI sequences. Here, we measure the relative heating of a MB protocol compared with a standard single-band (SB) protocol considered to be safe. We also evaluated EEG quality recorded concurrently with the MB protocol on humans. We compared radiofrequency (RF)-related heating at multiple electrodes and magnetic field magnitude, B_(1+RMS), of a MB fMRI sequence with whole-brain coverage (TR = 440 ms, MB factor = 4) against a previously recommended, safe SB sequence using a phantom outfitted with a 64-channel EEG cap. Next, 9 human subjects underwent eyes-closed resting state EEG-fMRI using the MB sequence. Additionally, in three of the subjects resting state EEG was recorded also during the SB sequence and in an fMRI-free condition to directly compare EEG data quality across scanning conditions. EEG data quality was assessed by the ability to remove gradient and cardioballistic artifacts along with a clean spectrogram. The heating induced by the MB sequence was lower than that of the SB sequence by a factor of 0.73 ± 0.38. This is consistent with an expected heating ratio of 0.64, calculated from the square of the ratio of B_(1+RMS) values of the sequences. In the resting state EEG data, gradient and cardioballistic artifacts were successfully removed using traditional template subtraction. All subjects showed an individual alpha peak in the spectrogram with a posterior topography characteristic of eyes-closed EEG. The success of artifact rejection for the MB sequence was comparable to that in traditional SB sequences. Our study shows that B_(1+RMS) is a useful indication of the relative heating of fMRI protocols. This observation indicates that simultaneous EEG-fMRI recordings using this MB sequence can be safe in terms of RF-related heating, and that EEG data recorded using this sequence is of acceptable quality after traditional artifact removal techniques

Multimodal population brain imaging in the UK Biobank prospective epidemiological study

Medical imaging has enormous potential for early disease prediction, but is impeded by the difficulty and expense of acquiring data sets before symptom onset. UK Biobank aims to address this problem directly by acquiring high-quality, consistently acquired imaging data from 100,000 predominantly healthy participants, with health outcomes being tracked over the coming decades. The brain imaging includes structural, diffusion and functional modalities. Along with body and cardiac imaging, genetics, lifestyle measures, biological phenotyping and health records, this imaging is expected to enable discovery of imaging markers of a broad range of diseases at their earliest stages, as well as provide unique insight into disease mechanisms. We describe UK Biobank brain imaging and present results derived from the first 5,000 participants' data release. Although this covers just 5% of the ultimate cohort, it has already yielded a rich range of associations between brain imaging and other measures collected by UK Biobank

Monileikekuvantamisen karakterisointi multifokaalisen näköärsykkeen avulla

Simultaneous multi-slice (SMS) echo-planar imaging (EPI) is an imaging technique that can be used to accelerate the imaging speed of a functional magnetic resonance imaging (fMRI) scan and increase the temporal resolution of the data acquisition. SMS EPI is already a widely evaluated imaging technique but its benefits for task-based fMRI are still unclear. The aim of this Thesis is to comprehensively characterise SMS EPI sequence using a multifocal stimulus paradigm. The multifocal fMRI mapping technique is a retinotopic mapping method that enables to map the activation cluster of multiple regions in a short time. The effects of preselected slice acceleration factors, fMRI paradigm repetition times (TR), flip angles and the use of generalized autocalibrating partially parallel acquisition (GRAPPA) acceleration are evaluated. In addition, the possibility to improve the multifocal fMRI mapping method with SMS EPI is examined. The multifocal fMRI data were acquired with six different protocols. The repetition time (TR) of the reference protocol was 1800 ms. With different slice acceleration factors, the TR was shortened to be 900, 720, 400, 360 and 240 ms. Ten healthy subjects were measured with all six protocols. For half of the subjects, the flip angles were optimised with Ernst angle and for the others, the flip angle was chosen to be a constant 60 degrees. The SMS EPI sequences were characterised by calculating local signal-to-noise ratios (SNR) and maximum t-statistics. Between protocols the achieved activation clusters (size and location) and multifocal maps were compared. Overall, shorter TRs increase statistical power, although a radical reduction of the TR decreases the SNR significantly. Even the TR of 240 ms results in reasonable data quality. The use of simultaneous GRAPPA acceleration has negative effects to the data quality, and optimised flip angles give significantly better outcomes than unoptimised flip angles. These results indicate that moderate slice acceleration factors have benefits to multifocal fMRI.Monileikekuvantaminen (SMS EPI) on kuvantamismenetelmä, joka mahdollistaa useamman leikkeen kuvantamisen samanaikaisesti ja siten lyhentää magneettikuvauksen kokonaisaikaa. Menetelmää on käytetty paljon erilaisissa tutkimuksissa, mutta sen mahdollisia hyötyjä ja haittoja tutkitaan edelleen. Tämän työn yhtenä tavoitteena on kokonaisvaltaisesti karakterisoida SMS EPI -sekvenssiä multifokaaliärsykkeen avulla. Käytetty multifokaalimenetelmä on retinotooppinen kartoitusmenetelmä, jonka avulla näköalueita kartoitetaan. Työssä tutkitaan, mikä vaikutus eri kiihdytyskertoimilla, käytetyllä toistoajalla (TR), flippikulman suuruudella ja mahdollisella GRAPPA-kiihdytyksellä on. Lisäksi tutkitaan, onko SMS EPI -sekvenssin avulla mahdollista parantaa jo valmiiksi optimoitua multifokaalimenetelmää. Multifokaalidata kerättiin erilaisilla protokollilla, joissa käytetyt toistoajat lyhennettiin eri kiihdytyskertoimien avulla. Kiihdytyskertoimettoman vertailusekvenssin TR oli 1800 ms. Muissa protokollissa kiihdytyskertoimien avulla TR lyhennettiin 900, 720, 400, 360 ja 240 ms:iin. Kymmenen tervettä koehenkilöä mitattiin kaikilla protokollilla. Puolet koehenkilöistä mitattiin käyttäen Ernstin kulmalla optimoituja flippikulmia. Muiden koehenkilöiden kohdalla flippikulma asetettiin olemaan 60 astetta riippumatta käytetyistä protokollista. Eri SMS EPI -sekvenssit karakterisoitiin laskemalla paikallinen signaali-kohina suhde (SNR) ja t-testin t-arvoja. Lisäksi aktivaatioklustereiden kokoa ja sijaintia sekä saatuja multifokaalikarttoja verattiin protokollien välillä toisiinsa. Kokonaisuudessaan työ osoittaa, että lyhyempi TR antaa tilastollista hyötyä, vaikka sen radikaalinen lyhentäminen selkeästi pienentää SNR:ää. Kuitenkin jopa 240 ms toistoajalla saatiin vielä luotettavia tuloksia. Lisäksi työ osoittaa, että optimoiduilla flippikulmilla on positiivinen vaikutus tuloksiin. GRAPPA-kiihdytyksen samanaikainen käyttö leikekiihdytyksen kanssa vaikuttaa dataan negatiivisesti. Työ osoittaakin, että kohtuullisesta kiihdytyskertoimesta on hyötyä näköalueiden multifokaalikartoitukselle toiminnallisen magneettikuvauksen (fMRI) avulla