Hi Bing,<br><br>1) Manual ROI approach<br>Many papers use manual ROI approach and it's still one of the best ways. The downside is, you have to be an expert neuroanatomist and even so, the ROI placement reproducibility is often a concern.<br>
<br>For the manual ROI approach, you can use the DtiStudio "ROI" tab, but I recommend you to use RoiEditor, which has a much stronger interface.<br><br>Using DtiStudio, you need to load an FA map to get FA values. You can directly draw ROIs on an FA map in the "ROI" tab and determine the average FA within the ROI. You can also load both color and FA map, draw ROIs on the color map, and measure FA. In this case, first choose the color map as an active image in the display in the "Image" tab, go to the "ROI" tab, draw an ROI, go back to the "Image" tab, choose the FA map as an active image, and go back to the "ROI" tab to find the FA value.<br>
<br>Using RoiEditor, you need to grasp the concept of "Object", which allows drawing of multiple 3D ROIs. Our manual is still weak, but you can find some in <a href="http://www.mristudio.org">www.mristudio.org</a>. There is also a video of our tutorial.<br>
<br>2) Automated ROI<br>You can use our atlas with more than 170 pre-defined ROIs, warped to your data. For this approach, you need to get DiffeoMap and RoiEditor from <a href="http://www.mristudio.org">www.mristudio.org</a>. Also, please read our recent papers by Mori et al, and Oishi et al, all in NeuroImage. Again, there is online manual in <a href="http://www.mristudio.org">www.mristudio.org</a>.<br>
<br>3) fiber tracking<br>Once you successfully segment your brain, you can use the segmented regions as ROIs for fiber tracking.<br><br>#2 and #3 are a bit advanced usage of our tools. #2 could be figured out through our website, I believe. We are planning to have a tutorial in ISMRM this year. Hope you can join.<br>
<br>Susumu<br><br><div class="gmail_quote">On Sun, Feb 28, 2010 at 11:19 PM, <span dir="ltr"><<a href="mailto:7by3@queensu.ca">7by3@queensu.ca</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;">
Dear users:<br><br><font face="'PrimaSans BT,Verdana,sans-serif'">We are doing a DTI project and
planning to use DTIstudio. I have some questions hope you could help me
answer.<br><br>1. How could I define ROI? (we are interested in the DMN
brain structures, such as medial prefrontal cortex, medial temporal
lobe, PCC etc). I just do not know how can I find these areas in the
brain? Is there anyway that brain regions could be marked in the brain?
Do I need to use atlas or I can just find it from DTI studio? (Hope it
makes sense) <br><br>2. I want to get FA values. After clicking
tensor, color map etc. tab from DTImap. I could not find FA values.
Could you let me know how and where to find these FA values?<br><br>3.
We are also looking at the fiber tract. For example, we want to look at
the fiber tract from PCC to medial temporal lobe. Therefore, we need to
find the seed region PCC. But how can I find the location of PCC in the
brain? (this question is similar to question 1). <br><br>Could you help me with these questions?<br><br>Thank you!<br><br>Bing</font><br>
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