Hi Bin,<div><br></div><div>To save a file as "Binary Map", you have to open it as ROI, not as an image. There are two "open" icons in the right column of RoiEditor; one for image and the other for ROI.</div>
<div><br></div><div>To access to these icons, you first have to open an image. The image can be anything as long as it has the same image dimension. For example, you can open the ROI file as an image, get the viewing window, and then open the same file as an ROI file.</div>
<div><br></div><div>Then you can save the ROI as "Binary Map".</div><div><br></div><div>Susumu</div><div><br></div><div><br><br><div class="gmail_quote">2011/2/28 bin wang <span dir="ltr"><<a href="mailto:binwang87828@gmail.com">binwang87828@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Dr Mori:<div>Thank you for the patience to answer, I will try as you say.</div><div>But there is still a question that I can't save it as "Binary Map" after loading the mask image to RoiEditor, I must draw a ROI manually or using other ways. I want to know that can I make the mask as a ROI directly, so the ROIEditor can save it.</div>
<div>Best</div><div>bin<br><br><div class="gmail_quote">在 2011年2月27日 下午7:31，susumu mori <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>></span>写道：<div><div></div><div class="h5">
<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br><br><div class="gmail_quote">2011/2/27 bin wang <span dir="ltr"><<a href="mailto:binwang87828@gmail.com" target="_blank">binwang87828@gmail.com</a>></span><div><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dr Mori:<div>I have two questions:</div><div>(1). If I want to create a 3D ROI, Must I draw the ROI in every slice in ROIEditor manually<span>?</span></div></blockquote><div><br></div></div><div>If the structure of interest has clear contrast, you can use a region growing tool. For example the caudate in T1 has a good contrast. You can use 3D or slice-by-slice region growing tool to define it much easier than manual. When you are using DTI colormap, there is a color region growing tool to specify a region with the same color.</div>
<div><br></div><div>If does not have clear contrast, you can first use the global threshold or region growing to define a tissue of interest. For example, if you are interested in a white matter structure, you can use FA>0.25. If you are interested in the cortex, you can use a threshold tool with T1. Please note that white matter structures and the cortex do not have clear contrast boundary from adjacent structures. Therefore the region growing or thresholding almost always leak to adjacent structures. After you do the global tissue segmentation, you can visit each slice and use manual ROI + AND operation to define the structure.</div>
<div><br></div><div>If you get tired of defining a lot of ROIs without clear boundaries, please try our automated full-brain segmentation tools. You need to learn how to use DiffeoMap and RoiEditor. You can find manuals and videos in <a href="http://www.mristudio.org" target="_blank">www.mristudio.org</a>.</div>
<div>
<div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>(2). I have a binary mask image(img/hdr), it is the calcarine regions of the brain, I want to make a ROI of the region to track the fiber in this region, and how can I do in ROIEditor or DTIstudio.</div>
</blockquote><div><br></div></div><div>You can load it to RoiEditor as an ROI file and save as "Binary Map". Please refer to FAQ16 about Binary Map format.</div><div><div></div><div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>Thanks in advance</div><div>Bin</div><div><br><div class="gmail_quote">在 2011年2月27日 上午12:10，susumu mori <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>></span>写道：<div>
<div></div><div><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Yes, RoiEditor can draw 3D ROIs. Because the ROI drawing capability of DtiStudio is limited, I recommend to use RoiEditor. It is possible to create multiple 3D ROIs in RoiEditor and pass them DtiStudio for fiber tracking. Please refer to FAQ16 in <a href="https://www.mristudio.org/wiki/faq" target="_blank">https://www.mristudio.org/wiki/faq</a>.<br>
<br><div class="gmail_quote">2011/2/26 bin wang <span dir="ltr"><<a href="mailto:binwang87828@gmail.com" target="_blank">binwang87828@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div></div><div>
Hello DTIstudio user:<div>I am a new DTIStudio user, I want to know if the ROIEditor can drawing a 3D ROI, and how to operation?</div><div>bin</div><div><br>-- <br><div>
<div><font face="arial,helvetica,sans-serif" color="#000000" size="1">++++++++++++++++++++++++++++++<br>Bin Wang</font></div>
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<div><font face="arial,helvetica,sans-serif" color="#000000" size="1">major：apply psychology</font></div>
<div><font face="arial,helvetica,sans-serif" color="#000000" size="1">South China Normal University<br>Zhongshan Avenue West 55, Tianhe District<br>Guangzhou 510631<br>P. R. China<br>Tel: 13416157706</font></div>
<div><font face="arial,helvetica,sans-serif" color="#000000" size="1">++++++++++++++++++++++++++++++<br>王斌<br>华南师范大学 </font></div>
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<div><font color="#000066"><font face="arial,helvetica,sans-serif"><font size="1"><font color="#000000"><strong> 地址：<br></strong>广东省 广州市 天河区 中山大道 西55号<br>邮编：510631<br>电话： 13416157706 (手机, 广州)<br>+++++++++++++++++++++++++</font></font><br>
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