slice diffusion weighted image data  (Bruker Corporation)

Journal: Brain imaging and behavior

Article Title: White matter abnormalities in mild traumatic brain injury with and without post-traumatic stress disorder: A subject-specific diffusion tensor imaging study

doi: 10.1007/s11682-017-9744-5

Figure Lengend Snippet: Diffusion weighted imaging (single shell) acquisition parameters

Article Snippet: For the present study, only the diffusion weighted imaging data were analyzed ; their acquisition parameters are listed in . table ft1 table-wrap mode="anchored" t5 caption a7 Sequence Parameters Philips Scanners 1 Orientation Axial Phase Encoding Direction anterior to posterior Field of view 256mm Bandwidth 1396Hz/Px Number of directions 87 b-value 900 Number of b0 7 Matrix size 128 × 128 Voxel size 2 × 2 × 2 Number of slices 73 Acquisition time 14m 08sec Open in a separate window 1 Identical parameters applied to both sites using Philips scanners Diffusion weighted imaging (single shell) acquisition parameters We first conducted a quality verification of our data.

Techniques: Diffusion-based Assay, Imaging

Journal: Journal of magnetic resonance imaging : JMRI

Article Title: In Utero Localized Diffusion MRI of the Embryonic Mouse Brain Microstructure and Injury

doi: 10.1002/jmri.24828

Figure Lengend Snippet: Use of selective excitation pulse and a 3D diffusion-weighted gradient spin-echo sequence (DW-GRASE) sequence for localized diffusion MRI. (A) Performance of the spatially selective excitation pulse was tested in an agarose gel phantom. The red box in the image of the phantom represents an 8 × 8 mm field of excitation. The yellow and blue curves in (B) show the excitation profile along the x-axis and y-axis, respectively. (C) A diagram of the 3D DW-GRASE sequence with spatially selective excitation pulse. The sequence can be extended to include two fields of excitation and acquisition. The diagram shows two localized imaging modules that target two separate embryos in an interleaved fashion. The localized imaging module is expanded to show the timing of the 2D selective excitation pulse together with the spiral gradient in the x–y plane, diffusion sensitization, the GRASE readout, and the twin-navigator echoes. Each GRASE readout acquires five double-sampled gradient and spin echoes and is repeated four times to achieve an acceleration factor of 20 compared to the conventional spin echo sequence. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Article Snippet: All MRI experiments are summarized in and described as follows. table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 MRI Protocol Receiver coil used Resolution (mm) TE/TR (ms) Diffusion encoding Scan time (min) SNR In utero DWI Body coil 0.20 isotropic 21/1000 2 b 0 + 6 DWI, b = 800 s/mm 2 34 23.7 ± 3.6 In utero T 2 -weighted Surface coil 0.13 isotropic 24/1000 N/A 10 28.9 In utero DTI Surface coil 0.20 isotropic 0.16 isotropic 21/500 23/500 4 b 0 + 30 DWI, b = 1000 s/mm 2 72 113 26.2 ± 3.8 23.3 Ex vivo DTI Volume coil 0.20 isotropic 0.16 isotropic 21/500 23/500 4 b 0 + 30 DWI, b = 1000 s/mm 2 72 113 197.5 ± 11.1 173.6 Open in a separate window Imaging Parameters Used for T 2 -Weighted Imaging, DWI, and DTI of the E17 Embryonic Mouse Brain Diffusion-weighted imaging (DWI) data were acquired from E17 embryos (nine LPS-treated embryos from three pregnant dams, and four sham-treated embryos from two pregnant dams) using an 8-channel phased array receive-only rat body coil (Bruker Biospin), which covered the entire abdomen.

Techniques: Diffusion-based Assay, Sequencing, Agarose Gel Electrophoresis, Imaging

Journal: Journal of magnetic resonance imaging : JMRI

Article Title: In Utero Localized Diffusion MRI of the Embryonic Mouse Brain Microstructure and Injury

doi: 10.1002/jmri.24828

Figure Lengend Snippet: Motion correction based on twin-navigator echo phase correction and retrospective image registration. Navigator echo phase correction improves image quality by removing motion artifacts, eg, smearing of structural boundaries (indicated by the arrowheads), in both nondiffusion-weighted images (A) and diffusion-weighted images (B). Rigid image registration corrects motion-induced misalignment between images. For example, mismatch between Image #1 and Image #2 can be corrected after registration (C). (D) Translational motions of five embryonic mouse brains were estimated based on rigid transformations and plotted over a 1-hour period. Horizontal axis denotes scan time in minutes, and vertical axis denotes the translational movements in mm. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Article Snippet: All MRI experiments are summarized in and described as follows. table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 MRI Protocol Receiver coil used Resolution (mm) TE/TR (ms) Diffusion encoding Scan time (min) SNR In utero DWI Body coil 0.20 isotropic 21/1000 2 b 0 + 6 DWI, b = 800 s/mm 2 34 23.7 ± 3.6 In utero T 2 -weighted Surface coil 0.13 isotropic 24/1000 N/A 10 28.9 In utero DTI Surface coil 0.20 isotropic 0.16 isotropic 21/500 23/500 4 b 0 + 30 DWI, b = 1000 s/mm 2 72 113 26.2 ± 3.8 23.3 Ex vivo DTI Volume coil 0.20 isotropic 0.16 isotropic 21/500 23/500 4 b 0 + 30 DWI, b = 1000 s/mm 2 72 113 197.5 ± 11.1 173.6 Open in a separate window Imaging Parameters Used for T 2 -Weighted Imaging, DWI, and DTI of the E17 Embryonic Mouse Brain Diffusion-weighted imaging (DWI) data were acquired from E17 embryos (nine LPS-treated embryos from three pregnant dams, and four sham-treated embryos from two pregnant dams) using an 8-channel phased array receive-only rat body coil (Bruker Biospin), which covered the entire abdomen.

Techniques: Diffusion-based Assay

Journal: Journal of magnetic resonance imaging : JMRI

Article Title: In Utero Localized Diffusion MRI of the Embryonic Mouse Brain Microstructure and Injury

doi: 10.1002/jmri.24828

Figure Lengend Snippet: (A) T2-weighted images of an embryonic mouse brain acquired at 0.13 mm isotropic resolution. The ventricles were reconstructed in 3D based on the high-contrast T2-weighted images. (B) In vivo DTI of an E17 embryonic mouse brain at 0.2 mm isotropic resolution, in comparison with ex vivo DTI result (C) at the same resolution. Several gray and white matter structures in the E17 mouse brain can be delineated in the FA maps (top rows) and direction-encoded colormaps (bottom rows), eg, the cortical plate (CP), intermediate zone (IZ), cerebral peduncle (cp), internal capsule (ic), optic tract (opt), and fimbria (fi).

Article Snippet: All MRI experiments are summarized in and described as follows. table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 MRI Protocol Receiver coil used Resolution (mm) TE/TR (ms) Diffusion encoding Scan time (min) SNR In utero DWI Body coil 0.20 isotropic 21/1000 2 b 0 + 6 DWI, b = 800 s/mm 2 34 23.7 ± 3.6 In utero T 2 -weighted Surface coil 0.13 isotropic 24/1000 N/A 10 28.9 In utero DTI Surface coil 0.20 isotropic 0.16 isotropic 21/500 23/500 4 b 0 + 30 DWI, b = 1000 s/mm 2 72 113 26.2 ± 3.8 23.3 Ex vivo DTI Volume coil 0.20 isotropic 0.16 isotropic 21/500 23/500 4 b 0 + 30 DWI, b = 1000 s/mm 2 72 113 197.5 ± 11.1 173.6 Open in a separate window Imaging Parameters Used for T 2 -Weighted Imaging, DWI, and DTI of the E17 Embryonic Mouse Brain Diffusion-weighted imaging (DWI) data were acquired from E17 embryos (nine LPS-treated embryos from three pregnant dams, and four sham-treated embryos from two pregnant dams) using an 8-channel phased array receive-only rat body coil (Bruker Biospin), which covered the entire abdomen.

Techniques: In Vivo, Comparison, Ex Vivo

Journal: Journal of magnetic resonance imaging : JMRI

Article Title: In Utero Localized Diffusion MRI of the Embryonic Mouse Brain Microstructure and Injury

doi: 10.1002/jmri.24828

Figure Lengend Snippet: Apparent Diffusion Coefficient (ADC) and Fractional Anisotropy (FA) of Several Gray And White Structures Measured From the In Vivo and Ex Vivo E17 Embryonic Mouse Brains ( n = 5)

Article Snippet: All MRI experiments are summarized in and described as follows. table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 MRI Protocol Receiver coil used Resolution (mm) TE/TR (ms) Diffusion encoding Scan time (min) SNR In utero DWI Body coil 0.20 isotropic 21/1000 2 b 0 + 6 DWI, b = 800 s/mm 2 34 23.7 ± 3.6 In utero T 2 -weighted Surface coil 0.13 isotropic 24/1000 N/A 10 28.9 In utero DTI Surface coil 0.20 isotropic 0.16 isotropic 21/500 23/500 4 b 0 + 30 DWI, b = 1000 s/mm 2 72 113 26.2 ± 3.8 23.3 Ex vivo DTI Volume coil 0.20 isotropic 0.16 isotropic 21/500 23/500 4 b 0 + 30 DWI, b = 1000 s/mm 2 72 113 197.5 ± 11.1 173.6 Open in a separate window Imaging Parameters Used for T 2 -Weighted Imaging, DWI, and DTI of the E17 Embryonic Mouse Brain Diffusion-weighted imaging (DWI) data were acquired from E17 embryos (nine LPS-treated embryos from three pregnant dams, and four sham-treated embryos from two pregnant dams) using an 8-channel phased array receive-only rat body coil (Bruker Biospin), which covered the entire abdomen.

Techniques: Diffusion-based Assay, In Vivo, Ex Vivo

Journal: Journal of magnetic resonance imaging : JMRI

Article Title: In Utero Localized Diffusion MRI of the Embryonic Mouse Brain Microstructure and Injury

doi: 10.1002/jmri.24828

Figure Lengend Snippet: (A) In vivo T2-weighted images (T2w), DWI, and ADC maps of three E17 embryonic mouse brains at 6 hours after intrauterine injection of LPS. The images were acquired at 0.2 mm resolution using the localized DW-GRASE sequence. Yellow and blue arrows indicate cortical and subcortical injury (reduced T2 intensity and ADC) in these mice, respectively. (B) Nissl and H&E-stained sections at similar levels as the MR images, from a control embryo and an LPS-treated embryo. The LPS-treated embryo showed reduced cortical thickness (red arrows, including the cortex plate, subplate, intermediate zone, and ventricular zone) and shrunken neurons (insets), compared to the control embryo. The black arrowheads point to the normal and shrunken cytoplasm in the cortical neurons. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Article Snippet: All MRI experiments are summarized in and described as follows. table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 MRI Protocol Receiver coil used Resolution (mm) TE/TR (ms) Diffusion encoding Scan time (min) SNR In utero DWI Body coil 0.20 isotropic 21/1000 2 b 0 + 6 DWI, b = 800 s/mm 2 34 23.7 ± 3.6 In utero T 2 -weighted Surface coil 0.13 isotropic 24/1000 N/A 10 28.9 In utero DTI Surface coil 0.20 isotropic 0.16 isotropic 21/500 23/500 4 b 0 + 30 DWI, b = 1000 s/mm 2 72 113 26.2 ± 3.8 23.3 Ex vivo DTI Volume coil 0.20 isotropic 0.16 isotropic 21/500 23/500 4 b 0 + 30 DWI, b = 1000 s/mm 2 72 113 197.5 ± 11.1 173.6 Open in a separate window Imaging Parameters Used for T 2 -Weighted Imaging, DWI, and DTI of the E17 Embryonic Mouse Brain Diffusion-weighted imaging (DWI) data were acquired from E17 embryos (nine LPS-treated embryos from three pregnant dams, and four sham-treated embryos from two pregnant dams) using an 8-channel phased array receive-only rat body coil (Bruker Biospin), which covered the entire abdomen.

Techniques: In Vivo, Injection, Sequencing, Staining, Control