[Mristudio-users] ROI placement

[susumu mori]

1) If you do a lot of ROI drawing, I recommend you to move to RoiEditor you
can download from www.mristudio.org. It has a seamless interface between
DtiStudio and has much stronger functions for ROI drawing.
2) When you draw ROIs, there are two ways;
a: draw ROIs in individual images such that you define the corresponding
structures among different subjects
b: draw the same ROI (the same size, shape, and location) and change the
shapes of the subjects. If eveybody's shape becomes the same, you draw an
ROI only once and can apply it to everybody else.

The latter is, as you know, called brain normalization. DiffeoMap, which
also can be downloaded from www.mristudio.org, provides several tools for
the brain normalization.
Once you normalize your images into the shape of our template (atlas), you
can also use our pre-defined sets of ROIs, called White Matter Parcellation
Maps (WMPM). In these maps, white matter and gray matter strucutres are
pre-segmented (50-176 regions depending on the type of WMPM). You can apply
these pre-defined ROIs to the normalized images.

If you are interested in all these, I recoomend you to read;

Mori S.,* *Oishi K., Jiang H, Jiang L., Li X., Akhter K., Hua K., Faria AV.,
Mahmod A., Woods R., Toga WA., Pike B, Rosa Neto P, Evans A, Zhang J, Huang
H, Miller MI, van Zijl, PCM, Mazziotta, J, "Stereotaxic white matter atlas
based on diffusion tensor imaging in an ICBM template", NeuroImage, 40,
570-582(2008)

Oishi K, Zilles K, Amunts K, Faria A, Jiang H, Li X, Akhter K, Hua K, Woods
R, Toga AW, Pike GB, Posa-Neto P, Evans A, Zhang J, Huang H, Mikker MI, van
Zijl PCM, Mazziotta J, Mori S, "Human brain white matter atlas:
identification and assignment of common anatomical structures in superficial
white matter", Neuroimage, 43, 447-457 (2008)

Oishi K, Faria A, Jiang H, Li X, Akhter K, Zhang J, Hsu J, Miller MI, van
Zijl PCM, Albert M, Lyketsos CG, Woods R, Toga AW, Pike GB, Rosa-Neto P,
Evans A, Mazziotta J, Mori S, "Atlas-based whole brain white matter analysis
using large deformation diffeomorphic metric mapping: Application to normal
elderly and Alzheimers' disease participants", Neuroimage, 46, 486-499
(2009)

There are a nice "Getting Started" for the DiffeoMap section of
www.mristudio.org, but our manuals are not ready yet. You can ask questions
to the forum in www.mristudio.org.

Susumu

On Fri, Dec 11, 2009 at 11:56 AM, Demitry Kazlouski <dima_mk at hotmail.com>wrote:

> Hello,
>
>
>
> Can someone suggest me a better way to place ROI(s) within a white matter
> tract and get accurate FAs (fractional anisotropy values) for a group
> comparison?
>
> I see two ways by using ROI tab. One is to place ROI of a fixed shape for
> all subjects. The other way is to create manually drawn ROIs. If I use the
> first method, there would be some uncertainty because the fibers of other
> white matter tracts might be selected. If I use the second method, my ROIs
> would have different areas and, I assume, this would affect FA values. It
> seems like both methods have pros and cons. Please let me know your
> opinion.
> Thanks.
>
>
>
>
>
> Demitry Kazlouski, BS
>
> Research Assistant, Developmental Brain Research Program University of
> Colorado Denver
>
> The Children's Hospital, Gary Pavilion A036/B-130
>
> 13123 East 16th Avenue
>
> Aurora, CO 80045
>
>  <mailto:dima_mk at hotmail.com> dima_mk at hotmail.com
>
>
>
>
>
>
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