Mapping of whole-cerebrum resting-state networks using ultra-high resolution acquisition protocols.

Resting-state functional magnetic resonance imaging (fMRI) has been used in numerous studies to map networks in the brain that employ spatially disparate regions. However, attempts to map networks with high spatial resolution have been hampered by conflicting technical demands and associated problems. Results from recent fMRI studies have shown that spatial resolution remains around 0.7 × 0.7 × 0.7 mm3 , with only partial brain coverage. Therefore, this work aims to present a novel fMRI technique that was developed based on echo-planar-imaging with keyhole (EPIK) combined with repetition-time-external (TR-external) EPI phase correction. Each technique has been previously shown to be effective in enhancing the spatial resolution of fMRI, and in this work, the combination of the two techniques into TR-external EPIK provided a nominal spatial resolution of 0.51 × 0.51 × 1.00 mm3 (0.26 mm3 voxel) with whole-cerebrum coverage. Here, the feasibility of using half-millimetre in-plane TR-external EPIK for resting-state fMRI was validated using 13 healthy subjects and the corresponding reproducible mapping of resting-state networks was demonstrated. Furthermore, TR-external EPIK enabled the identification of various resting-state networks distributed throughout the brain from a single fMRI session, with mapping fidelity onto the grey matter at 7T. The high-resolution functional image further revealed mesoscale anatomical structures, such as small cerebral vessels and the internal granular layer of the cortex within the postcentral gyrus.

Perfusion weighted imaging using combined gradient/spin echo EPIK: Brain tumour applications in hybrid MR-PET.

Advanced perfusion-weighted imaging (PWI) methods that combine gradient echo (GE) and spin echo (SE) data are important tools for the study of brain tumours. In PWI, single-shot, EPI-based methods have been widely used due to their relatively high imaging speed. However, when used with increasing spatial resolution, single-shot EPI methods often show limitations in whole-brain coverage for multi-contrast applications. To overcome this limitation, this work employs a new version of EPI with keyhole (EPIK) to provide five echoes: two with GEs, two with mixed GESE and one with SE; the sequence is termed "GESE-EPIK." The performance of GESE-EPIK is evaluated against its nearest relative, EPI, in terms of the temporal signal-to-noise ratio (tSNR). Here, data from brain tumour patients were acquired using a hybrid 3T MR-BrainPET scanner. GESE-EPIK resulted in reduced susceptibility artefacts, shorter TEs for the five echoes and increased brain coverage when compared to EPI. Moreover, compared to EPI, EPIK achieved a comparable tSNR for the first and second echoes and significantly higher tSNR for other echoes. A new method to obtain multi-echo GE and SE data with shorter TEs and increased brain coverage is demonstrated. As proposed here, the workflow can be shortened and the integration of multimodal clinical MR-PET studies can be facilitated.

Dynamic susceptibility contrast parametric imaging using accelerated dual-contrast echo planar imaging with keyhole.

BACKGROUND: Echo planar imaging (EPI) is one of the methods of choice in dynamic susceptibility contrast MRI (DSC-MRI) because it provides a sufficient temporal resolution. However, the relatively long readout duration of EPI often imposes limitations on increased spatial coverage or the use of multiple contrasts. PURPOSE: To develop a DSC-MRI method using EPIK (EPI with keyhole) to provide dual-contrast (TE1 and TE2 ) information with a higher spatial coverage than EPI. To compare results from the community-standard EPI method and the proposed EPIK method. STUDY TYPE: Prospective. SUBJECTS: One healthy subject and 17 brain tumor patients. FIELD STRENGTH/SEQUENCE: 3 T/accelerated EPI and dual-contrast EPIK sequences. ASSESSMENT: After an initial evaluation using healthy in vivo images, the use of the proposed method for DSC-MRI was verified with brain tumor patients. The parametric images (eg, CBF and CBV) and arterial input function (AIF), obtained from both the EPI and EPIK, were compared. STATISTICAL TESTS: The ratio of AIF peak height of the proposed method to that of EPI was computed. The ratio computation was also performed for the time-to-peak (TTP) in the AIF curves. From the obtained CBF and CBV maps, the tumor-to-brain (TBR) ratio was also calculated for each imaging method and the results were compared. RESULTS: For the same temporal resolution (1.5 sec), EPIK yielded dual-contrast (TEs of 13/33 msec) with an increased spatial coverage (24 slices) and less geometric distortions than EPI; EPI provided single contrast (TE of 32 msec) with 20 slices. The obtained parametric values (eg, AIF peak, TTP, and TBR) had similar characteristics between EPI and the proposed method. DATA CONCLUSION: The dual-contrast data produced by EPIK in DSC-MRI allowed T1 -corrected parametric images without the need of second contrast injection and an enhanced estimation of the AIF. LEVEL OF EVIDENCE: 1 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2019;50:628-640.

Cortical depth-dependent human fMRI of resting-state networks using EPIK.

Introduction: Recent laminar-fMRI studies have substantially improved understanding of the evoked cortical responses in multiple sub-systems; in contrast, the laminar component of resting-state networks spread over the whole brain has been less studied due to technical limitations. Animal research strongly suggests that the supragranular layers of the cortex play a critical role in maintaining communication within the default mode network (DMN); however, whether this is true in this and other human cortical networks remains unclear. Methods: Here, we used EPIK, which offers unprecedented coverage at sub-millimeter resolution, to investigate cortical broad resting-state dynamics with depth specificity in healthy volunteers. Results: Our results suggest that human DMN connectivity is primarily supported by intermediate and superficial layers of the cortex, and furthermore, the preferred cortical depth used for communication can vary from one network to another. In addition, the laminar connectivity profile of some networks showed a tendency to change upon engagement in a motor task. In line with these connectivity changes, we observed that the amplitude of the low-frequency-fluctuations (ALFF), as well as the regional homogeneity (ReHo), exhibited a different laminar slope when subjects were either performing a task or were in a resting state (less variation among laminae, i.e., lower slope, during task performance compared to rest). Discussion: The identification of varied laminar profiles concerning network connectivity, ALFF, and ReHo, observed across two brain states (task vs. rest) has major implications for the characterization of network-related diseases and suggests the potential diagnostic value of laminar fMRI in psychiatric disorders, e.g., to differentiate the cortical dynamics associated with disease stages linked, or not linked, to behavioral changes. The evaluation of laminar-fMRI across the brain encompasses computational challenges; nonetheless, it enables the investigation of a new dimension of the human neocortex, which may be key to understanding neurological disorders from a novel perspective.

EPiK-a Workflow for Electron Tomography in Kepler.

Scientific workflows integrate data and computing interfaces as configurable, semi-automatic graphs to solve a scientific problem. Kepler is such a software system for designing, executing, reusing, evolving, archiving and sharing scientific workflows. Electron tomography (ET) enables high-resolution views of complex cellular structures, such as cytoskeletons, organelles, viruses and chromosomes. Imaging investigations produce large datasets. For instance, in Electron Tomography, the size of a 16 fold image tilt series is about 65 Gigabytes with each projection image including 4096 by 4096 pixels. When we use serial sections or montage technique for large field ET, the dataset will be even larger. For higher resolution images with multiple tilt series, the data size may be in terabyte range. Demands of mass data processing and complex algorithms require the integration of diverse codes into flexible software structures. This paper describes a workflow for Electron Tomography Programs in Kepler (EPiK). This EPiK workflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered backprojection (FBP) from TxBR and iterative reconstruction methods. We have tested the three dimensional (3D) reconstruction process using EPiK on ET data. EPiK can be a potential toolkit for biology researchers with the advantage of logical viewing, easy handling, convenient sharing and future extensibility.