1) If you do a lot of ROI drawing, I recommend you to move to RoiEditor you can download from <a href="http://www.mristudio.org">www.mristudio.org</a>. It has a seamless interface between DtiStudio and has much stronger functions for ROI drawing.<br>
2) When you draw ROIs, there are two ways;<br>a: draw ROIs in individual images such that you define the corresponding structures among different subjects<br>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.<br>
<br>The latter is, as you know, called brain normalization. DiffeoMap, which also can be downloaded from <a href="http://www.mristudio.org">www.mristudio.org</a>, provides several tools for the brain normalization. <br>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.<br>
<br>If you are interested in all these, I recoomend you to read;<br><br><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 12"><meta name="Originator" content="Microsoft Word 12"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5CSusumu%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C04%5Cclip_filelist.xml"><link rel="themeData" href="file:///C:%5CDOCUME%7E1%5CSusumu%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C04%5Cclip_themedata.thmx"><link rel="colorSchemeMapping" href="file:///C:%5CDOCUME%7E1%5CSusumu%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C04%5Cclip_colorschememapping.xml"><style>
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<p class="MsoNormal" style="margin-left: 22pt; text-align: justify; text-indent: -22pt;"><span style="font-size: 10pt;">Mori S.,</span><b style=""><span style="font-size: 10pt;"> </span></b><span style="font-size: 10pt;">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)</span></p>
<br><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 12"><meta name="Originator" content="Microsoft Word 12"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5CSusumu%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C05%5Cclip_filelist.xml"><link rel="themeData" href="file:///C:%5CDOCUME%7E1%5CSusumu%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C05%5Cclip_themedata.thmx"><link rel="colorSchemeMapping" href="file:///C:%5CDOCUME%7E1%5CSusumu%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C05%5Cclip_colorschememapping.xml"><style>
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</style><span style="font-size: 10pt; font-family: "Times","serif";">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)</span><br><br><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 12"><meta name="Originator" content="Microsoft Word 12"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5CSusumu%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C06%5Cclip_filelist.xml"><link rel="themeData" href="file:///C:%5CDOCUME%7E1%5CSusumu%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C06%5Cclip_themedata.thmx"><link rel="colorSchemeMapping" href="file:///C:%5CDOCUME%7E1%5CSusumu%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C06%5Cclip_colorschememapping.xml"><style>
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</style><span style="font-size: 10pt; font-family: "Times","serif";">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)</span><br><br>There are a nice "Getting Started" for the DiffeoMap section of <a href="http://www.mristudio.org">www.mristudio.org</a>, but our manuals are not ready yet. You can ask questions to the forum in <a href="http://www.mristudio.org">www.mristudio.org</a>.<br>
<br>Susumu<br><br><div class="gmail_quote">On Fri, Dec 11, 2009 at 11:56 AM, Demitry Kazlouski <span dir="ltr"><<a href="mailto:dima_mk@hotmail.com">dima_mk@hotmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
<br>
<br>
Can someone suggest me a better way to place ROI(s) within a white matter<br>
tract and get accurate FAs (fractional anisotropy values) for a group<br>
comparison?<br>
<br>
I see two ways by using ROI tab. One is to place ROI of a fixed shape for<br>
all subjects. The other way is to create manually drawn ROIs. If I use the<br>
first method, there would be some uncertainty because the fibers of other<br>
white matter tracts might be selected. If I use the second method, my ROIs<br>
would have different areas and, I assume, this would affect FA values. It<br>
seems like both methods have pros and cons. Please let me know your opinion.<br>
Thanks.<br>
<br>
<br>
<br>
<br>
<br>
Demitry Kazlouski, BS<br>
<br>
Research Assistant, Developmental Brain Research Program University of<br>
Colorado Denver<br>
<br>
The Children's Hospital, Gary Pavilion A036/B-130<br>
<br>
13123 East 16th Avenue<br>
<br>
Aurora, CO 80045<br>
<br>
<mailto:<a href="mailto:dima_mk@hotmail.com">dima_mk@hotmail.com</a>> <a href="mailto:dima_mk@hotmail.com">dima_mk@hotmail.com</a><br>
<br>
<br>
<br>
<br>
<br>
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