Hi Joanne,<div><br></div><div>Please see;</div><div><span style="font-size:11.0pt;font-family:"Times New Roman","serif";
mso-fareast-font-family:"MS Mincho";mso-ansi-language:EN-US;mso-fareast-language:
JA;mso-bidi-language:AR-SA">Zhang YJ, Zhang JY, Oishi K, Faria AV, Jiang HY, Li
X, Akhter K, Rosa-Neto P, Pike GB, Evans A, Toga AW, Woods R, Mazziotta JC,
Miller MI, van Zijl PCM, Mori S. Atlas-guided tract reconstruction for
automated and comprehensive examination of the white matter anatomy. NeuroImage
2010;52(4):1289-1301. PMC2910162</span><br><br>This paper describes the same idea.</div><div>If you want to use WMPM as ROIs, you first have to register it to each subject.</div><div>Assuming the registration is good, you can turn the WMPM into ROIs by the following procedure;</div>
<div><br></div><div>1) Read the WMPM as an image, not as ROI into RoiEditor</div><div>2) By placing the cursor to a pacellated region of interest, you can read the assigned value. For example, the splenium of the CC is "119".</div>
<div>3) Use the threshold tool and choose pixels with a value "119". This operation selects all pixels in the splenium of the CC.</div><div>4) Register the selected pixels as "Object 1".</div><div>5) Repeat the procedure to the second region of interest and register the selected pixels to "Object 2".</div>
<div>6) Once you define all regions of interest as separate Objects, save the Objects (the "save" icon in the "ROI" section) as "Binary Map"</div><div>7) Read FAQ15 at <a href="https://www.mristudio.org/wiki/faq">https://www.mristudio.org/wiki/faq</a> to learn how to use Binary Map for fiber tracking in DtiStudio. You can combine multiple ROIs with AND/OR/NOT operations.</div>
<div><br></div><div>For many white matter tracts, we already generated combinations of parcels defined in the WMPM (e.g. a combination for CST, SLF, etc), which can be registered to each patient and ready for fiber tracking. I believe these WMPM-ROI files are posted somewhere in our website. Please contact Yajing for more detail.</div>
<div><br></div><div>Susumu</div><div><br><div class="gmail_quote">On Wed, Nov 9, 2011 at 11:24 PM, Joanne Lin <span dir="ltr"><<a href="mailto:joanne.lin@auckland.ac.nz">joanne.lin@auckland.ac.nz</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div lang="EN-NZ" link="blue" vlink="purple">
<div>
<p class="MsoNormal">Hi all,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I have a question about saving ROIs from ROIEditor and then using them for tractography.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I was hoping to perform tractography for each of my participants, but because my anatomy knowledge is limited, I wanted to avoid having to manually delineating regions. I have processed the data so the JHU_MNI_SS_WMPM_TypeII is in diffusion
space; my question is this – is it valid to use one (or more) of these atlas-defined structures as ROIs for tractography?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">If so, how can I isolate and save one (or more) of the atlas regions as a single ROI on its own? I have tried ‘hide all’ and unhiding the one/s I am interested it but it doesn’t appear to work. Apart from deleting all of the (many) structures
I’m not interested in, is there a way to do this properly?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Also, is ‘binary map’ the best format to save ROIs to use in fibre tracking?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Any advice greatly appreciated. Thank you kindly for your help! <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Kind regards,<u></u><u></u></p>
<p class="MsoNormal">Jo<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-family:"Georgia","serif";color:#00B0F0">Joanne Lin<u></u><u></u></span></b></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Georgia","serif"">BPharm (Hons), RegPharmNZ<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Georgia","serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Georgia","serif"">Pharmacist/PhD Candidate<br>
School of Pharmacy<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Georgia","serif"">Faculty of Medical & Health Sciences<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Georgia","serif"">The University of Auckland<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Georgia","serif"">Private Bag 92019<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Georgia","serif"">Auckland, New Zealand<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Georgia","serif""><a href="tel:%2B64%209%20373%207599%20Ext%2088468" value="+6493737599" target="_blank">+64 9 373 7599 Ext 88468</a></span><span style="font-size:10.0pt"><u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
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