We trained, validated, and tested the wave-MoDL using three different databases acquired on a 3T Siemens Prisma system equipped with a 32-channel head receive array. Table 1 shows the acquisition parameters of the databases and the networks. Figure 2 shows the g-factor analyses of SENSE and wave-CAIPI, linear reconstructions with neither network nor regularization, at the target acceleration for each database. We separated the 3D data into slice groups and trained on sets of aliasing slices to address the GPU memory constraint. The number of slices of an input 3D batch image is equal to the acceleration factor in the slice-encoding direction. For example, at , a batch contains three slices that are aliasing on each other slice and need to be unaliased. Multiple contrast images were concatenated in the input channel dimension of the network. The wave-MoDL network updates the results during 10 outer iterations and takes 10 conjugate gradients per iteration in the data consistency layers. The unrolled CNN has five hidden layers consisting of a 24-depth filter with a leaky ReLU activation per layer, and all network parameters were zero-initialized. Coil sensitivity maps were calculated from external 3D low-resolution gradient-echo-based reference scans using ESPIRiT [4 (link)]. Example code can be found at https://github.com/jaejin-cho/wave-modl (accessed on 4 April 2022).
Prisma system
Manufactured by Siemens
Sourced in Germany
The Prisma system is a laboratory equipment product offered by Siemens. It is designed to perform core functions within a laboratory setting. The product specifications and technical details are maintained in an objective and concise manner without any interpretation or extrapolation.
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21 protocols using prisma system
1
Accelerated MRI Reconstruction with wave-MoDL
2
Resting-State fMRI Acquisition Protocol
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All MRIs were acquired on a 3.0 Tesla Siemens Prisma System (Siemens Medical
Solutions, Erlangen, Germany) using a 12-channel head matrix coil. Structural
images were obtained utilizing a 3-dimenstional T1 sequence (TR = 2300 ms,
TI = 900 ms, TE =3.5 ms, flip angle = 9 degrees, field of view = 24 cm,
acquisition matrix 256 × 256 × 176, slice thickness =1 mm. Functional
T2*-weighted blood-oxygen-level-dependent (BOLD) images for resting state fMRI
(rs-fMRI) were acquired using 2-dimensional gradient echo echo-planar imaging
(TR = 2000 ms, TE = 30 ms, flip angle 90 degrees, field of view 24 cm,
acquisition matrix 64 × 64 × 33, slice thickness = 4 mm, slice gap = 1 mm,
interleaved acquisition). Moreover, 300 volumes (10 min) of rs-fMRI data were
acquired. Participants were instructed to stay as motionless as possible, not
think of anything in particular, and keep eyes open for the duration of the
scan.
Solutions, Erlangen, Germany) using a 12-channel head matrix coil. Structural
images were obtained utilizing a 3-dimenstional T1 sequence (TR = 2300 ms,
TI = 900 ms, TE =3.5 ms, flip angle = 9 degrees, field of view = 24 cm,
acquisition matrix 256 × 256 × 176, slice thickness =1 mm. Functional
T2*-weighted blood-oxygen-level-dependent (BOLD) images for resting state fMRI
(rs-fMRI) were acquired using 2-dimensional gradient echo echo-planar imaging
(TR = 2000 ms, TE = 30 ms, flip angle 90 degrees, field of view 24 cm,
acquisition matrix 64 × 64 × 33, slice thickness = 4 mm, slice gap = 1 mm,
interleaved acquisition). Moreover, 300 volumes (10 min) of rs-fMRI data were
acquired. Participants were instructed to stay as motionless as possible, not
think of anything in particular, and keep eyes open for the duration of the
scan.
3
Multimodal Brain Imaging Protocol
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We used a 3-Tesla MRI system (Prisma system; Siemens, Erlangen, Germany) with a 64-channel head coil. Anatomical images were obtained using a three-dimensional T1-weighted Magnetization-Prepared Rapid-Gradient Echo sequence (repetition time [TR] = 1,900 ms, echo time [TE] = 2.9 ms, inversion time [TI] = 960 ms, and flip angle = 9°, 1 × 1 × 1-mm resolution). The acquisition time was 5 min 50 s. We performed rs-fMRI using a two-dimensional gradient echo-planar sequence (TR = 2,500 ms, TE = 30 ms, and flip angle = 80°), voxel size = 3.3 × 3.3 × 3.2 mm, and acquisition time = 10 min. The patients were instructed to remain awake and to look at one point. We adopted an auto-discarding system that scanned the first 10 volumes and discarded them to allow for magnetic field stabilization.
4
Gd2O3@PCD-Glu NPs Targeting Ability
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In order to evaluate the targeting ability of Gd2O3@PCD-Glu NPs in in-vitro, MDA-MB-231 cells (of density = 1 × 106 cells/well)
were seeded into 6-well plates with 2 ml fresh medium. It was incubated afterwards at 37°C and 5% CO2 overnight to achieve cell confluence.
This was later substituted with a fresh non-glucose medium (2 mL) with PBS (control), Gd2O3@PCD-Glu with Gd+3 concentrations of 0, 12.5,
and 50 μg/mL. Cells were incubated at 37°C and 5% CO2 for a further 6 h. The choice of Gd+3 concentrations was according to the acceptable cytotoxicity of the MTT assay.
Then, the cells were washed with PBS 5 times, trypsinized, centrifuged, and resuspended in 1 ml PBS (containing 0.5% agarose) in 2 ml Eppendorf tubes for MR imaging.
A 3 T Siemens Prisma system was used for all MR imaging. Conventional spin-echo sequence with the following inputs: TR/TE =500/12 ms, 220 × 320 matrices,
82× 120 mm field of view, 140 Hz/Px of bandwidth, and slice thickness of 3 mm was used for the acquisition of T1-weighted images [ 11 (link)
].
were seeded into 6-well plates with 2 ml fresh medium. It was incubated afterwards at 37°C and 5% CO2 overnight to achieve cell confluence.
This was later substituted with a fresh non-glucose medium (2 mL) with PBS (control), Gd2O3@PCD-Glu with Gd+3 concentrations of 0, 12.5,
and 50 μg/mL. Cells were incubated at 37°C and 5% CO2 for a further 6 h. The choice of Gd+3 concentrations was according to the acceptable cytotoxicity of the MTT assay.
Then, the cells were washed with PBS 5 times, trypsinized, centrifuged, and resuspended in 1 ml PBS (containing 0.5% agarose) in 2 ml Eppendorf tubes for MR imaging.
A 3 T Siemens Prisma system was used for all MR imaging. Conventional spin-echo sequence with the following inputs: TR/TE =500/12 ms, 220 × 320 matrices,
82× 120 mm field of view, 140 Hz/Px of bandwidth, and slice thickness of 3 mm was used for the acquisition of T1-weighted images [ 11 (link)
].
5
Neuroimaging Volumetric Analysis Protocol
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Anatomical predictor variables included the volumetric measure of frontal, parietal, medial temporal and occipital GM. Subjects underwent MRI in a whole body MR system which included a 3T Siemens Tim Trio system (Siemens, Erlangen, Germany) and a 3T Siemens Prisma system (Siemens, Erlangen, Germany). Voxel-based morphometry was conducted using the Computational Anatomy Toolbox (CAT12) package for the Statistical Parametric Mapping 12 (SPM12) software (http://www.fil.ion.ucl.ac.uk/spm ) in MATLAB. Volumetric MPRAGE sequences were converted from DICOM to 3D NIFTI format and manually oriented to be within the standard Montreal Neurological Institute template space. Images were segmented into GM and cerebrospinal fluid maps using a unified segmentation pipeline (22 (link)), including affine regularization to the International Consortium for Brain Mapping space template for East Asian brains, bias corrections, and affine and non-linear modulated normalization. The generated GM maps were then smoothed (8 mm full width at half maximum) in SPM12. CAT12 was used to estimate the total intracranial volume for each subject, and the smoothed GM maps were used to generate global volumes of GM, and also regional volumes based on regions of interest defined using the Wake Forest University Pick Atlas v3.0 software toolbox (23 (link)).
6
Longitudinal MRI Assessment of Canine MPS IIIB
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MRI evaluations were conducted on MPS IIIB and unaffected littermate dogs from Table 1 over six sessions, starting at approximately 8 months of age (session 1) and ending at 24 months of age (session 6, Supplemental Fig. 1A ). The intervening sessions occurred approximately every 3 months. MRI acquisition (three-dimensional, high-resolution, T1-weighted magnetization-prepared rapid gradient-echo pulse sequence) was performed on a 3 Tesla Siemens Prisma system with Tx/Rx 15-channel knee coil at the University of Minnesota, Twin Cities. Logistical constraints prevented collection of data from some animals and limited data collection on other animals. Volumes assessed included total brain, cerebral white matter, cerebral gray matter, ventricles, brainstem, cerebellar white matter, and cerebellar gray matter volumes. Total cerebellum and brainstem were manually outlined following the canine atlas (Singer 1962 ). After brain extraction using FSL brain extraction tool (Jenkinson et al., 2012 (link)) and manual correction of brain extraction tool inaccuracies, cerebral and cerebellar subvolumes were derived using FSL FAST (FMRIB’s Automated Segmentation Tool) (Zhang et al., 2001 (link)). All MRI data were collected and analyzed by individuals blinded to the genotype and treatment status of the dogs.
7
Ex Vivo Brain Imaging of Diverse Species
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The MaMI database includes a total of 225 ex vivo diffusion and T2- and T1-weighted brain scans of 125 different animal species (Figure 1—figure supplement 1 ). No animals were deliberately euthanized for this study. All brains were collected based on incidental death of animals in zoos in Israel or natural death collected abroad, and with the permission of the national park authority (approval no. 2012/38645) or its equivalent in the relevant countries. All scans were performed on excised and fixated tissue. Animals’ brains were extracted within 24 hr of death and placed in formaldehyde (10%) for a fixation period of a few days to a few weeks (depending on the brain size). Approximately 24 hr before the MRI scanning session, the brains were placed in phosphate-buffered saline for rehydration. Given the limited size of the bore, small brains were scanned using a 7-T 30/70 BioSpec Avance Bruker system, whereas larger brains were scanned using a 3-T Siemens Prisma system. To minimize image artefacts caused by magnet susceptibility effects, the brains were immersed in fluorinated oil (Flourinert, 3M) inside a plastic bag during the MRI scanning session.
8
High-Resolution 3T MRI Protocol
9
Functional MRI Data Acquisition and Preprocessing
10
High-Resolution Structural MRI Acquisition
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Structural MRI scan was performed using a 3.0-T Siemens Prisma system equipped with a 64-channel head coil at the Shanghai Key Laboratory of Magnetic Resonance (East China Normal University, Shanghai, China). Subjects were instructed not to move to minimize head movement, close their eyes, and relax during the scan. High-resolution T1-weighted anatomical images were obtained by using a fast-acquisition gradient-echo pulse sequence prepared by 3D magnetization with the following parameters: repetition time = 2,530 ms, echo time = 2.98 ms, inversion time = 1,100 ms, flip angle = 7°, number of slices = 192, sagittal orientation, field of view = 256 × 256 mm2, and voxel size = 1 × 1 × 1 mm3. As previously reported, the mean frame-wise displacement (FD) was calculated during head movement processing (Li et al., 2020 (link)). Subjects with mean FD Jenkinson greater than 0.2 were excluded.
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