Three Dimensional Digital Mouse Atlas Using μMRI S.W. Ruffins, M. Dhenain, & R.E. Jacobs Biological Imaging Center, Beckman Institute, Caltech, Pasadena, CA 91125 Gene expression patterns, receptor domains, arrays of innervation, cell lineage patterns, and a host of other types of information in the embryo and adult take place in 3 spatial and 1 temporal dimensions. They occur within the context of the specific specimen being examined. Digital atlases provide a means to place specific data within the context of normal anatomy, analyze the information in multiple dimensions, and examine relationships between different types of information. In this work we present a prototypical digital atlas of the mouse embryo based on microscopic Magnetic Resonance Imaging (μMRI). μMRI is a qualitatively different, although complementary, imaging method to those used in constructing atlases with classical histological techniques. It is able to non-invasively and in 3 dimensions distinguish soft tissues within optically op...

We used functional MRI to study cerebellar activity during three bimanual coordination tasks: Syncopation at 1.33Hz and synchronization at 1.33Hz and 2.66Hz. Previous research (EEG & MEG) shows that spatiotemporal patterns of brain activation depend on both coordination frequency and the mode of coordination (syncopation or synchronization). Participants coordinated bimanual finger-thumb opposition either on-the-beat (synchronize) or in-between two consecutive beats (syncopate). We used the noise (pings) produced by the scanner (Signa 1.5T, GE Inc.) as auditory stimuli. The repetition time (TR) and number of slices was set in each condition such that the pings took place at the desired frequency, i.e. at 1.33Hz and 2.66Hz. Behavioral performance was monitored as pressure changes in two small air pillows which the subjects were holding between the thumb, and the index and middle finger of each hand. This signal was compared to the time points of pulses produced by the scanner when taking a slice. Results sh...

Introduction: We studied the remote subcortical effects of cortical damage in twenty-one patients affected by stroke due to embolic occlusion of the left middle cerebral artery. We hypothesized that damage of cortical gray matter would result in decrease of volumes in subcortical remote brain areas such as the thalamus or the corpus striatum that are connected to these cortical regions. Methods: The neuroimaging protocol included rapid volumetric homogenization of the magnetic field (shimming) over the entire brain volume and 3D Morphometric images (GE SPGR inversion recovery weighted T1 images). This protocol was performed successfully in twenty-one patients affected by stroke and twenty normal control subjects. Results and Discussion: We observed volumetric reduction of subcortical gray structures in the patients, especially ipsilateral to the cortical lesions. Here we report the raw data for the thalamus as an example of our findings. In the normal control young adults the mean value of the right thalam...

19 Participants with developmental Specific Language Impairment (SLI) were examined by neuropsychological and quantitative magnetic resonance imaging (MRI) techniques. Measures of intelligence (IQ), language, and memory were obtained, and 3D MRI structural datasets were analysed for bilateral pathology using voxel-based morphometry (VBM). Each participant had been diagnosed with SLI during childhood, and had or was attending a special language unit. The participants ranged in age between 8 and 24 years, and none had any evidence of oro-motor dyspraxia. In addition, each had superior nonverbal compared to verbal IQ, and was impaired on a range of language tests, and on measures of episodic long term memory. To examine the reliability of the VBM findings, two age-matched SLI groups (N=10, & N=9) were formed. Using VBM, comparison of each group to its own control group (matched on age, sex, and nonverbal IQ) showed significant bilateral reductions in grey matter within the cerebellum, particularly around the ...

We propose that the rate of increase of the brain concentration of sodium, [Na+]br, monitored using sodium MRI, can be used to locate the ischemic region in a rat model of cortical ischemia. In four Sprague-Dawley rats, focal cortical ischemia was induced during isoflurane anesthesia and continuous physiological monitoring. Sodium 3D and proton 2D data were acquired on a 3 Tesla whole body scanner (GEMS) using a dual tuned 5 cm diameter coil. [Na+]br time course maps were acquired continuously from 2-7 hr after occlusion. T2-weighted proton images (T2w, see Fig) and MAP2 immuno-stained brain sections were used to verify the location of the infarct (red outline). AMIDE software was used to view, analyze, and register image data, including a parametric image of the rate of [Na+]br increase (color scale). For all four animals the region of maximal [Na+]br increase corresponded to the ischemic region identified with MAP2. [Na+]br increased at a population mean rate of 19 ± 2.4 %/hr in ischemic tissue (p = 0.00...

The cingulate gyrus, a brain area important for certain cognitive functions, is pathologically involved in the very early stages of Alzheimer’s disease. In this study we investigated the extent of change in this region as a function of healthy aging. Participants consisted of: 1) 41 elderly individuals with normal cognition (mean age: 79.1, range: 67-89); and 2) 27 young adults (mean age: 28.1, range: 22-35). They all underwent a high resolution MRI scan. The cingulate gyrus was segmented from 1.6 mm gapless T1 weighted images using the protocol described by Killiany et al. (Ann Neurol., 2000). For each hemisphere, the volumes of the cingulate gyrus and cortex were derived separately. To correct for individual differences in brain size, the volumes of regions of interest were divided by total intracranial volume. The young participants differed significantly from the old in normalized total (right+left) cingulate gyrus (p<0.001) and cortex (p<0.001) volumes. Further analyses indicated that these age-relate...

Brain slices provide a controllable in situ model for investigating the biophysical basis of water diffusion in nervous tissue. Yet only acute studies are possible because brain slices seldom remain viable beyond 12 hrs due to cell death processes initiated by procurement. This limitation may be overcome by developing diffusion MRI methods for organotypic cultures, which remain viable for many weeks. In the present study, hippocampal slices were procured from P7 rat pups and cultured for 10 days on Millipore culture plate inserts. The inserts then were placed into an NMR tube and imaged using a 15mm birdcage coil in a 750-MHz wide-bore spectrometer. Although the small volume of cultured slices (~ 0.8 mm3) limited available signal-to-noise (S/N), in 1 slice, 8 diffusion-weighted images with b values between 56 and 3970 s/mm2 were obtained with S/N ratios of at least 18. As a first approximation, biexponential analysis of diffusion-weighted signal attenuation in this slice resulted in values of 0.54 for Ffas...

Functional magnetic resonance imaging (fMRI) and electroencephalography (EEG) are two noninvasive methods commonly used to study neural mechanisms supporting visual attention in humans. Studies using these tools, which have complementary spatial and temporal resolutions, implicitly assume they index similar underlying neural modulations related to external stimulus and internal attentional manipulations. Accordingly, they are often used interchangeably for constraining understanding about the impact of bottom-up and top-down factors on neural modulations. To test this core assumption, we simultaneously manipulated bottom-up sensory inputs by varying stimulus contrast and top-down cognitive modulations by changing the focus of spatial attention. Each of the male and female subjects participated in both fMRI and EEG sessions performing the same experimental paradigm. We found categorically different patterns of attentional modulation on fMRI activity in early visual cortex and early stimulus-evoked potential...

Precise characterization of cerebellar anatomic subdivisions is required for functional and structural imaging studies of the cerebellum. Volumetric changes during normal development and aging, or related to pathology, emphasize the relevance of morphometric cerebellar cortical analysis. In addition, localization of functional imaging activation in human cerebellar cortex is aided by precise mapping of function onto structural anatomy. We describe a parcellation system of the human cerebellar cortex based upon neuroanatomy which conserves the topographic uniqueness of the individual brain and allows volumetric measurements of specific parcellation units (PUs) of the cerebellar cortex using T1 MRI. METHODS: Based upon a set of fissures, we have defined a system for parcellation of the human cerebellar hemispheres and the vermis into well defined, closed areas or PUs. To this end, eleven fissures and two splines were required. To apply this method to T1-weighted anatomic MR images, cerebellar cortical exteri...

Blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI) has become a pivotal tool in localizing brain functions in vivo. However, despite its wide application in basic and clinical sciences, the electrophysiological basis of the BOLD signals remains elusive. Likewise, the precise spatial congruence between the foci of neuronal and BOLD activity remains controversial. The overall objective of this study is to define the neural correlate of BOLD by performing combined fMRI and single unit recordings in a single subject. We used a 4.7T horizontal bore scanner (Oxford, UK) to label the individual iso-orientation columns in cat primary visual cortex. Animal preparation and stimulation paradigms were similar to those of standard optical imaging experiments. A dense Cartesian grid phantom was placed on the exposed cortex for the fMRI and single-unit signal alignment. Typical MR parameters were: gradient-echo echo-planar images; TE=31ms; TR=0.5 sec; 64×64 or 128×128; FOV=2×2 cm2 (nomi...