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Identification and characterisation of midbrain nuclei using optimised functional magnetic resonance imaging.

ABSTRACT: Localising activity in the human midbrain with conventional functional MRI (fMRI) is challenging because the midbrain nuclei are small and located in an area that is prone to physiological artefacts. Here we present a replicable and automated method to improve the detection and localisation of midbrain fMRI signals. We designed a visual fMRI task that was predicted would activate the superior colliculi (SC) bilaterally. A limited number of coronal slices were scanned, orientated along the long axis of the brainstem, whilst simultaneously recording cardiac and respiratory traces. A novel anatomical registration pathway was used to optimise the localisation of the small midbrain nuclei in stereotactic space. Two additional structural scans were used to improve registration between functional and structural T1-weighted images: an echo-planar image (EPI) that matched the functional data but had whole-brain coverage, and a whole-brain T2-weighted image. This pathway was compared to conventional registration pathways, and was shown to significantly improve midbrain registration. To reduce the physiological artefacts in the functional data, we estimated and removed structured noise using a modified version of a previously described physiological noise model (PNM). Whereas a conventional analysis revealed only unilateral SC activity, the PNM analysis revealed the predicted bilateral activity. We demonstrate that these methods improve the measurement of a biologically plausible fMRI signal. Moreover they could be used to investigate the function of other midbrain nuclei.

SUBMITTER: Limbrick-Oldfield EH

PROVIDER: S-EPMC3236997 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Parkinson disease (PD) is a chronic progressive neurodegenerative disorder characterized pathologically by early loss of neuromelanin (NM) in the substantia nigra pars compacta (SNpc) and increased iron deposition in the substantia nigra (SN). Degeneration of the SN presents as a 50 to 70% loss of pigmented neurons in the ventral lateral tier of the SNpc at the onset of symptoms. Also, using magnetic resonance imaging (MRI), iron deposition and volume changes of the red nucleus (RN), and subthalamic nucleus (STN) have been reported to be associated with disease status and rate of progression. Further, the STN serves as an important target for deep brain stimulation treatment in advanced PD patients. Therefore, an accurate in-vivo delineation of the SN, its subregions and other midbrain structures such as the RN and STN could be useful to better study iron and NM changes in PD. Our goal was to use an MRI template to create an automatic midbrain deep gray matter nuclei segmentation approach based on iron and NM contrast derived from a single, multiecho magnetization transfer contrast gradient echo (MTC-GRE) imaging sequence. The short echo TE = 7.5 ms data from a 3D MTC-GRE sequence was used to find the NM-rich region, while the second echo TE = 15 ms was used to calculate the quantitative susceptibility map for 87 healthy subjects (mean age ± SD: 63.4 ± 6.2 years old, range: 45-81 years). From these data, we created both NM and iron templates and calculated the boundaries of each midbrain nucleus in template space, mapped these boundaries back to the original space and then fine-tuned the boundaries in the original space using a dynamic programming algorithm to match the details of each individual's NM and iron features. A dual mapping approach was used to improve the performance of the morphological mapping of the midbrain of any given individual to the template space. A threshold approach was used in the NM-rich region and susceptibility maps to optimize the DICE similarity coefficients and the volume ratios. The results for the NM of the SN as well as the iron containing SN, STN, and RN all indicate a strong agreement with manually drawn structures. The DICE similarity coefficients and volume ratios for these structures were 0.85, 0.87, 0.75, and 0.92 and 0.93, 0.95, 0.89, 1.05, respectively, before applying any threshold on the data. Using this fully automatic template-based deep gray matter mapping approach, it is possible to accurately measure the tissue properties such as volumes, iron content, and NM content of the midbrain nuclei.

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Project description:BACKGROUND:The use of functional connectivity magnetic resonance imaging (fcMRI) in research involving preterm infants is relatively new, and its feasibility in this population is not fully established. However, fcMRI images reveal functional neural connections that may be useful in establishing the mechanisms of neuroprotective interventions in preterm infants. OBJECTIVE:The aim of this study was to determine the feasibility of using fcMRI to measure differences in functional neural connections in nursing intervention studies. METHODS:A pilot study was conducted as part of a longitudinal, randomized controlled trial (RCT) testing the effect of a feeding intervention on neurodevelopmental and clinical outcomes of preterm infants randomly assigned to one of two groups: a patterned feeding experience (PFE) group and a usual feeding care (UFC) group. The fcMRIs were done at term-equivalent age. Visual, motor, and default mode networks were analyzed. RESULTS:Seven infants were studied (four were in the PFE group, and three were in the UFC group). Participants were selected sequentially from the parent RCT. Clear images were obtained from all participants. Differences were noted among PFE and UFC infants: Infants receiving PFE were hyperconnective in the default mode (caudate, anterior cingulate cortex, and precuneus) and motor networks (middle temporal and middle occipital areas) and hypoconnective in others areas of the default mode (hippocampal and lingual regions) and motor networks (precentral and superior frontal cortices) relative to UFC infants. No differences were noted in visual networks. DISCUSSION:The feasibility of using fcMRI at term-equivalent age in preterm infants who participated in an RCT on the effect of a nursing intervention was shown. Differences in connectivity among infants by group were detected. Further research is needed to show the benefit of fcMRI in studies of preterm infants given the costs of the procedure as well as the uncertain relationship of this early outcome measure to long-term neurodevelopment.

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Identification and characterisation of midbrain nuclei using optimised functional magnetic resonance imaging.

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