Robust preprocessing for stimulus-based functional MRI of the moving fetus

Abstract

Abstract. Fetal motion manifests as signal degradation and image artifact in the acquired time series of blood oxygen level dependent (BOLD) functional magnetic resonance imaging (fMRI) studies. We present a robust preprocessing pipeline to specifically address fetal and placental motion-induced artifacts in stimulus-based fMRI with slowly cycled block design in the living fetus. In the proposed pipeline, motion correction is optimized to the experimental paradigm, and it is performed separately in each phase as well as in each region of interest (ROI), recognizing that each phase and organ experiences different types of motion. To obtain the averaged BOLD signals for each ROI, both misaligned volumes and noisy voxels are automatically detected and excluded, and the missing data are then imputed by statistical estimation based on local polynomial smoothing. Our experimental results demonstrate that the proposed pipeline was effective in mitigating the motion-induced artifacts in stimulus-based fMRI data of the fetal brain and placenta.

T2*‐weighted placental MRI: basic research tool or emerging clinical test for placental dysfunction?

“…In addition, three animal studies described changes in placental signal intensity during maternal hypoxia, normoxic hypercapnia and injection of a vasoconstrictor. Human studies were performed at both 1.5 T and 3 T using single‐shot GE‐EPI sequences. However, the specific echo‐time (TE) and repetition time (TR) varied between studies (Table S1).…”

Spatiotemporal alignment of in utero BOLD‐MRI series

“…In particular, rigid body motion can be assumed for brain, so lower thresholds were set for brain where lower expansion or compression is expected when nonrigid body motion correction is applied. While the fraction of outliers for brain after our method is higher than the rigid motion correction approach, after the outlier rejection step the standard deviation of the brain signal along first normoxia epoch is significantly lower compared to the baseline rigid motion correction approach, which can be critical for the analysis of the brain response to the oxygenation change. Our results for fetal brain were not compared with the more sophisticated approaches previously proposed .…”

“…Second, the approach was tested in a limited number of subjects. Another limitation is that the processing time of our proposed method is an order of magnitude slower than the approach proposed previously . Computational efficiency was not the main focus of this study, and will be addressed by future work.…”

“…We evaluated the proposed intervolume motion correction method by quantifying the alignment of ROI delineations. We demonstrated improved anatomical alignment over a baseline rigid motion correction algorithm …”

Linear convolution model of fetal circulation for hemodynamic responses to maternal hyperoxia using in utero functional MRI

“…Using the region-of-interest (ROI) masks, all volumes were registered to the reference volume through rigid/non-rigid image registration of the Image Registration ToolKit (IRTK). Significantly misaligned volumes were automatically removed and the missing volumes were reconstructed through data imputation [5]. The voxel-wise BOLD signals were finally averaged over each ROI.…”