[ExI] High resolution MRI

Wed Jul 11 20:20:58 UTC 2007

And actually, I just realized the authors have another article which might
be more relevant than the one I just linked:

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-4NS2GHH-B&_user=1010281&_coverDate=05%2F18%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050264&_version=1&_urlVersion=0&_userid=1010281&md5=7ee12fd37f3f16b1609426fd70b456d4

Title: "High-throughput morphologic phenotyping of the mouse brain with
magnetic resonance histology"

Abstract: The Mouse Biomedical Informatics Research Network (MBIRN) has been
established to integrate imaging studies of the mouse brain ranging from
three-dimensional (3D) studies of the whole brain to focused regions at a
sub-cellular scale. Magnetic resonance (MR) histology provides the entry
point for many morphologic comparisons of the whole brain. We describe a
standardized protocol that allows acquisition of 3D MR histology (43-μm
resolution) images of the fixed, stained mouse brain with acquisition times
< 30 min. A higher resolution protocol with isotropic spatial resolution of
21.5 μm can be executed in 2 h. A third acquisition protocol provides an
alternative image contrast (at 43-μm isotropic resolution), which is
exploited in a statistically driven algorithm that segments 33 of the most
critical structures in the brain. The entire process, from specimen
perfusion, fixation and staining, image acquisition and reconstruction,
post-processing, segmentation, archiving, and analysis, is integrated
through a structured workflow. This yields a searchable database for archive
and query of the very large (1.2 GB) images acquired with this standardized
protocol. These methods have been applied to a collection of both male and
female adult murine brains ranging over 4 strains and 6 neurologic knockout
models. These collection and acquisition methods are now available to the
neuroscience community as a standard web-deliverable service.

On 7/11/07, Neil Halelamien <neilh at caltech.edu> wrote:
>
> Also, some of the things which distinguish this from a typical clinical
> MRI and various other notes:
>
> * unlike a lot of other mouse brain MRI research, the brains were left
> inside the cranium, preventing structural distortion/damage
> * the brains were fixed and treated with an MRI contrast agent
> * they used a 9.4T magnet (in contrast, typical clinical MRI is maybe
> 1-3T)
> * if I understand correctly, algorithms were then used to automatically
> segment the different brain areas (33 total) apart from each other, and the
> area data from the 6 brains was combined to form the atlas
> * in general, the research is kind of neat, combining a number of
> already-existing techniques to create a useful atlas
>
> On 7/11/07, Neil Halelamien < neilh at caltech.edu> wrote:
> >
> > The NeuroImage article is here, although I think it requires an
> > institutional subscription:
> >
> > http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WNP-4NX8MST-7&_user=1010281&_coverDate=06%2F07%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050264&_version=1&_urlVersion=0&_userid=1010281&md5=0d9d038b1101b4c523e05e0c7cdcd4e3
> >
> >
> > Here's the abstract:
> > Magnetic resonance microscopy (MRM), when used in conjunction with
> > active staining, can
> > produce high-resolution, high-contrast images of the mouse brain. Using
> > MRM, we imaged in
> > situ the fixed, actively stained brains of C57BL/6J mice in order to
> > characterize the
> > neuroanatomical phenotype and produce a digital atlas. The brains were
> > scanned within the
> > cranium vault to preserve the brain morphology, avoid shape distortions,
> > and to allow an
> > unbiased shape analysis. The high-resolution imaging used a T1-weighted
> > scan at 21.5 mm
> > isotropic resolution, and an eight-echo multiecho scan, post-processed
> > to obtain an enhanced T2
> > image at 43 mm resolution. The two image sets were used to segment the
> > brain into 33
> > anatomical structures. Volume, area, and shape characteristics were
> > extracted for all segmented
> > brain structures. We also analyzed the variability of volumes, areas and
> > shape characteristics.
> > The coefficient of variation of volume had an average value of 7.0.
> > Average anatomical images
> > of the brain for both the T1 weighted and T2 images were generated,
> > together with an average
> > shape atlas, and a probabilistic atlas for 33 major structures. These
> > atlases, with their associated
> > metadata, will serve as baseline for identifying neuroanatomical
> > phenotypes of additional strains,
> > and mouse models now under study. Our efforts were directed toward
> > creating a baseline for
> > comparison with other mouse strains and models of neurodegenerative
> > diseases.
> >
> > On 7/10/07, John K Clark < jonkc at att.net> wrote:
> > >
> > > Some scientists at Duke University have made a MRI image of a mouse
> > > brain with "100,000 times higher resolution than a clinical MRI scan".
> > > 100,000!
> > >
> > > http://www.sciencedaily.com/releases/2007/07/070709145329.htm
> > >
> > >   John K Clark
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > extropy-chat mailing list
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> > > http://lists.extropy.org/mailman/listinfo.cgi/extropy-chat
> > >
> >
> >
>
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