In this study, a 3D digital atlas of the live mouse brain based on magnetic resonance microscopy (MRM) is presented. C57BL/6J adult mouse brains were imaged in vivo on a 9.4 Tesla MR instrument at an isotropic spatial resolution of 100 µm. With suffi cient signal-to-noise (SNR) and contrast-to-noise ratio (CNR), 20 brain regions were identifi ed. Several atlases were constructed including 12 individual brain atlases, an average atlas, a probabilistic atlas and average geometrical deformation maps. We also investigated the feasibility of using lower spatial resolution images to improve time effi ciency for future morphological phenotyping. All of the new in vivo data were compared to previous published in vitro C57BL/6J mouse brain atlases and the morphological differences were characterized. Our analyses revealed signifi cant volumetric as well as unexpected geometrical differences between the in vivo and in vitro brain groups which in some instances were predictable (e.g. collapsed and smaller ventricles in vitro) but not in other instances. Based on these fi ndings we conclude that although in vitro datasets, compared to in vivo images, offer higher spatial resolutions, superior SNR and CNR, leading to improved image segmentation, in vivo atlases are likely to be an overall better geometric match for in vivo studies, which are necessary for longitudinal examinations of the same animals and for functional brain activation studies. Thus the new in vivo mouse brain atlas dataset presented here is a valuable complement to the current mouse brain atlas collection and will be accessible to the neuroscience community on our public domain mouse brain atlas website.

Mechanical vibrations of the gradient coil system during readout in echo-planar imaging (EPI) can increase the temperature of the gradient system and alter the magnetic field distribution during functional magnetic resonance imaging (fMRI). This effect is enhanced by resonant modes of vibrations and results in apparent motion along the phase encoding direction in fMRI studies. The magnetic field drift was quantified during EPI by monitoring the resonance frequency interleaved with the EPI acquisition, and a novel method is proposed to correct the apparent motion. The knowledge on the frequency drift over time was used to correct the phase of the k-space EPI dataset. Since the resonance frequency changes very slowly over time, two measurements of the resonance frequency, immediately before and after the EPI acquisition, are sufficient to remove the field drift effects from fMRI time series. The frequency drift correction method was tested "in vivo" and compared to the standard image realignment method. Growing demands on magnetic resonance imaging (MRI) systems to speed up image acquisition have led to the use of higher magnetic fields and to the development of ultrafast imaging techniques, e.g., echo planar imaging (EPI). Rapidly switched gradient fields during EPI-readout interact with the static magnetic field, producing strong timedependent mechanical forces in the gradient coil system that can stimulate natural modes of vibration in the coil assembly (1) and produce large vibrational amplitudes under on-resonance conditions (2).Friction between vibrating parts of the MRI scanner transforms mechanical vibration energy into heat, thereby increasing their temperature. Ferromagnetic shim elements frequently are attached to the vibrating gradient coil; therefore, vibrations can transiently increase their temperature and reduce their magnetization, which ultimately changes the homogeneity and strength of the local magnetic field. Even slight magnetic field shifts during EPI can lead to large apparent movements of the object in the phase encoding direction in functional MRI (fMRI) studies (3-6). If not corrected properly, such mismatches of the object's position in subsequent images may result in erroneous activation patterns in fMRI analyses (7,8).In this work we propose a simple approach to monitor the water resonance frequency during EPI experiments with interleaved one-dimension free-induction-decay (1D-FID) acquisitions, which provide high-resolution spectral information. We show that the frequency drift caused by vibration-related thermal effects, as observed in our system, is sufficiently slow in time; therefore, the instant frequency can be determined using two measures of the resonance frequency: immediately before and after the EPI time series and linear interpolation in between. We demonstrate that these measurements can be used to correct the observed frequency drift during EPI experiments by linear phase correction of the EPI k-space data. This approach does not significantly increase the overall scan ...

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Purpose: To present some unusual MR findings in a group of patients from the south-west of the Dominican Republic suffering from Pantothenate Kinase Associated Neurodegeneration (PKAN). Materials and Methods:Twenty patients and one preclinical case homozygous for the PANK2 mutation, 13 heterozygous gene carriers and 14 healthy volunteers were scanned prospectively using a 3 Tesla system.Results: All patients showed the typical signal reduction within the globus pallidus and the substantia nigra. A surprising finding was the absence of the bright spot (''tiger's eye'') in the medial part of the pallidum in 6 patients, but not in the preclinical case. Both fractional anisotropy (FA) and mean diffusivity (MD) were increased with high significance in the globus pallidus, whereas a reduction of FA in the anterior parts of the internal capsule was accompanied by an elevation of MD. Conclusion:Our findings support the hypothesis that the absence of the ''tiger's eye'' in PKAN might be secondary, probably caused by an increased accumulation of iron. This could artificially increase FA and MD values and change fiber tracking results. Except for the fronto-basal tracts, white matter was preserved well. This encouraging finding might support efforts to develop further therapeutic strategies in this devastating dystonia.

This work presents a novel approach to develop dedicated transverse gradient coils for head imaging. The proposed coil design is based on the stochastic optimization of an asymmetrical stream function and improves the matching between the region-of-interest and the homogeneous gradient volume. Additionally, the electric field produced by these asymmetrical coils is 30% lower than that produced by standard symmetrical designs, which minimizes the risk of magnetostimulation of nerves in fast imaging techniques. A prototype of the asymmetrical gradient coil was built to test the method and magnetic field produced by the prototype was measured.