I have been able finally to back project the ROIs for a single fasciculus and export them one by one. If you have an automatic TRS creation code (IDL or executables) that would make things much easier. I can maybe do as Yajing suggest, backproject the WMPM, but how to create the roi sets again without doing it one by one manually? This is something hopefully to do routinely for patients.<div>
<br></div><div>Thank you all.</div><div><br></div><div>Dorian<br><div><div><br><div class="gmail_quote">2013/1/31 Yajing Zhang <span dir="ltr"><<a href="mailto:zhangyajing9996@gmail.com" target="_blank">zhangyajing9996@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi, <div><br></div><div>I used IDL code for batch processing, and I think our executable functions can do the same thing. Because TRS is a set of labels of ROI in the WMPM type II, back-projection of TRS is corresponding to back-projection of the atlas parcellation map using Hmap (provided by LDDMM).</div>
<div><br></div><div>As for the ROI display, the intensity value is "1", so you can adjust the visualization scale as suggested below.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div><br></div>
<div>Yajing</div></font></span><div class="HOEnZb"><div class="h5"><div><br></div><div><br><div class="gmail_quote">
On Thu, Jan 31, 2013 at 2:37 PM, susumu mori <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Dorian,<div><br></div><div>I think it is just a matter of display intensity. The ROI locations have "1" and non-ROI pixels are "0". So, you have to right click on the image (looks like blank) and adjust the display intensity scale to see the dark ROIs (1 out of 256 grayscale is not visible).</div>
<div><br></div><div>As for the batch processing of TRS to each subject data, we have executable codes. </div><div>Xin and Hangyi, maybe we should post the executables somewhere in <a href="http://www.mristudio.org" target="_blank">www.mristudio.org</a>?</div>
<div><br></div><div>Yajing, how did you apply the TRS to each subject? Did you use IDL codes and the executables or did you use MriStudio one-by-one?<br><br><div class="gmail_quote">On Thu, Jan 31, 2013 at 12:46 PM, Dorian P. <span dir="ltr"><<a href="mailto:alb.net@gmail.com" target="_blank">alb.net@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<div><br></div><div>Just wanted to renovate this question. It is not clear to me how to backproject TRS files, or whether I should do it for the whole WMPM type II atlas.</div>
<div><br></div><div>The only way I could make atlas fiber tracking now is by projecting tensors in normalized and by manually creating a .map file for rois of a fasciculus. The TRS that are for download don't work in DTIstudio.</div>
<div><br></div><div>Thank you.</div><div><br></div><div>Dorian<br><br><div class="gmail_quote">2013/1/30 Dorian P. <span dir="ltr"><<a href="mailto:alb.net@gmail.com" target="_blank">alb.net@gmail.com</a>></span><div>
<div><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi all,<div><br></div><div>I am trying to do atlas based tract reconstruction based on Zhang Yajing (2010) paper. I have performed LDDMM and need to backproject a Template Roi Set (say the uncinate). The files in the TRS look like this: </div>
<div><br></div><div><div>ROI_display.roihdr</div><div>AND_#1.dat</div><div>NOT.dat</div><div>OR.dat</div><div>ROI_display.dat</div></div><div><br></div><div>I tried loading the these files in Diffeomap but there are no white pixels, all black. So, how ca I do this back projection?</div>
<div><br></div><div><br></div><div>And is there an automatic way to massively invert TRS's in native space or do I have to go one by one for each TRS to open and save in Diffeomap.</div><div><br></div><div><br></div>
<div>
Thank you.</div>
</blockquote></div></div></div><br></div>
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