Journal: PLoS Computational Biology

Article Title: Quantifying Differences and Similarities in Whole-Brain White Matter Architecture Using Local Connectome Fingerprints

doi: 10.1371/journal.pcbi.1005203

Figure Lengend Snippet: (A) The spin distribution function (SDF) calculated from diffusion MRI quantifies the density of diffusing water along axonal fiber bundles. The magnitudes of the SDF at axonal directions provide density-based measurements to characterize axonal fiber bundles. (B) The density measurements obtained from the SDFs show individuality between-subjects #1, #2, and #3 (intensity scaled between [0 0.8]). The density of diffusing water varies substantially across different portions of the corpus callosum. The repeat measurements after 238 (subject #1), 191 (subject #2), and 198 (subject #3) days present a consistent pattern that captures individual variability. (C) In contrast to the SDF shown in (B), the fractional anisotropy derived from diffusivity shows no obvious individuality between the same subjects #1, #2, and #3 (intensity also scaled between [0 0.8]). This is due to the fact that diffusivity, which quantifies how fast water diffuses, does not vary a lot in normal axonal bundles.

Article Snippet: Each subject had three diffusion MRI scans within 16 days on a Siemens Trio 3T system at the University of California, Santa Barbara.

Techniques: Diffusion-based Assay, Derivative Assay

Journal: PLoS Computational Biology

Article Title: Quantifying Differences and Similarities in Whole-Brain White Matter Architecture Using Local Connectome Fingerprints

doi: 10.1371/journal.pcbi.1005203

Figure Lengend Snippet: (A) Local connectome fingerprinting is conducted by first reconstructing diffusion MRI data into a standard space to calculate the spin distribution functions (SDFs). A common fiber direction atlas is then used to sample the density of diffusing water along the fiber directions in the cerebral white matter. The sampled measurements are compiled in a left-posterior-superior order to form a sequence of characteristic values as the local connectome fingerprint. (B) One local connectome fingerprint is shown in different zoom-in resolutions. A local connectome fingerprint has a total of 513,316 entries of scalar values. (C) The local connectome fingerprint of subject #1, #2, and #3 and their repeat measurements (lower row) after 238, 191, and 198 days, respectively. At a coarse level, the local connectome fingerprint differs substantially between three subjects, whereas those from the repeat scans show a remarkably identical pattern, indicating the uniqueness and reproducibility of the local connectome fingerprint.

Article Snippet: Each subject had three diffusion MRI scans within 16 days on a Siemens Trio 3T system at the University of California, Santa Barbara.

Techniques: Diffusion-based Assay, Sequencing

Journal: Translational Lung Cancer Research

Article Title: Magnetic resonance imaging in precision radiation therapy for lung cancer

doi: 10.21037/tlcr.2017.09.02

Figure Lengend Snippet: Characteristics of the most widely used MRI-guided radiotherapy treatment machines. Magnet strength (B 0 ) is reported with reference to the direction of the treatment beam ( 78 )

Article Snippet: The seven members of the Atlantic MR-Linac Consortium have purchased a clinical prototype developed by Elekta and Philips, which combines a 1.5 T wide bore MRI scanner with a 7 MV linear accelerator.

Techniques:

Journal: NeuroImage

Article Title: Ex Vivo Fetal Brain MRI: Recent Advances, Challenges, and Future Directions

doi: 10.1016/j.neuroimage.2019.03.034

Figure Lengend Snippet: Note that regions with FA values lower than 0.15–0.2 are observed in the majority (40 GW) and peripheral regions (3 years old) of the arcuate fasciculus that cannot be detected with popular DTI analysis methods with an FA threshold (Modified from Wilkinson et al., 2017, with permission). In addition to other technical issues including the quality of MRI scan acquisition and analysis, thresholding parameters based on FA values are important factors when performing tractography.

Article Snippet: The structural MRI scan is made available by the Allen Institute for Brain Science ( Miller et al. , 2014 ), and is available at: http://download.alleninstitute.org/brainspan/MRI_DTI_data_for_prenatal_specimens/ .

Techniques: Modification

Journal: NeuroImage

Article Title: Ex Vivo Fetal Brain MRI: Recent Advances, Challenges, and Future Directions

doi: 10.1016/j.neuroimage.2019.03.034

Figure Lengend Snippet: The GE wanes between GW 20 and 30. Coronal planes from a structural T1w MRI scans of a human at GW19 show cell dense regions consisting of the GE and cortical proliferative pool (CPP). Comparing the growth of these two proliferative pools throughout development in humans, macaques, and mice permits identifying evolutionary changes in neurogenesis timing across species. The structural MRI scan is made available by the Allen Institute for Brain Science (Miller et al., 2014), and is available at: http://download.alleninstitute.org/brainspan/MRI_DTI_data_for_prenatal_specimens/. Image credit: Allen Institute.

Article Snippet: The structural MRI scan is made available by the Allen Institute for Brain Science ( Miller et al. , 2014 ), and is available at: http://download.alleninstitute.org/brainspan/MRI_DTI_data_for_prenatal_specimens/ .

Techniques:

Journal: NeuroImage

Article Title: Ex Vivo Fetal Brain MRI: Recent Advances, Challenges, and Future Directions

doi: 10.1016/j.neuroimage.2019.03.034

Figure Lengend Snippet: (A) The timing of developmental transformations (expressed as age in days after conception in macaques and humans) is regressed against equivalent developmental transformations found in mice (Workman et al., 2013; Charvet et al., 2017b, Charvet and Finlay, 2018; Charvet et al., 2018). The timing of developmental transformations is instrumental in identifying corresponding ages across species. Such an approach permits identifying variation in the timing of select developmental processes after controlling for variation in developmental schedules across species. Using this approach, Charvet et al. (2017a) found that the ganglionic eminence (GE) (B) and cortical proliferative pool (C) grow for significantly longer in humans and macaques once overall differences in the duration of developmental schedules are controlled for (see Workman et al., 2013; Charvet et al., 2017a; Charvet and Finlay, 2018; Charvet et al., 2018). (D) Examples of equivalent developmental time points are shown from reconstructed structural MRI scans and micro CT-scans. Micro CT-scans of prenatal mice are from Wong et al., 2012. Structural MR scans of prenatal humans are from the multi-dimensional human embryo project (http://embryo.soad.umich.edu/index.html).

Article Snippet: The structural MRI scan is made available by the Allen Institute for Brain Science ( Miller et al. , 2014 ), and is available at: http://download.alleninstitute.org/brainspan/MRI_DTI_data_for_prenatal_specimens/ .

Techniques: Micro-CT