Hi, <div>I'm using the Siemens DICOM sample data set. I believe that I have to choose a y and z flip, as that combination yields the correct CST fibers when I put an ROI at the cerebral peduncle. </div><div>I see reasonable tracts when I use two ROIs with operation 0. There just seems to be a problem when using operation 1 for the second ROI, as there are a very small amount of fibers selected. </div>
<div>Thanks, </div><div><br></div><div>Deepa </div><div>
<br><div class="gmail_quote">On Sat, Feb 2, 2013 at 4:51 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">One potential reason is that your vector angles are not right.<div>First, please make sure that your DTI data have correct fiber orientations by using manual interactive ROI drawing and fiber tracking by DtiStudio. For example, you can define one ROI at the cerebral peduncle and make sure the CST trajectory reaches the motor cortex.</div>
<div><br></div><div>If you confirm that everything is working, then it could be the problem of your ROI file.</div><div>Do you see reasonable tracts when you use two ROIs with both operation: 0? </div><div>If so, then you can see what happens with Operation: 1 for the second ROI.<br>
<br><div class="gmail_quote"><div><div>On Wed, Jan 30, 2013 at 12:04 PM, Deepa Krishnaswamy <span dir="ltr"><<a href="mailto:deepa.krishnaswamy1@gmail.com" target="_blank">deepa.krishnaswamy1@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div>
Hi, <div>I have used the pipeline at <a href="https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_DualChannelNormalizationPipeline%3A" target="_blank">https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_DualChannelNormalizationPipeline%3A</a> to transform the sample Siemens DICOM data to the JHU_MNI_SS atlas. I am currently trying to segment the CST using the ROI operation rules listed in Table 1 of 'Atlas-guided tract reconstruction for automated and comprehensive examination of the white matter anatomy.' I've written my own ROI map file that specifies the ROIs and the operations. In Table 1, there are two ROIs listed, two additional AND ROIs, and a list of NOT ROIs. The syntax I have been using for part of the map file is below: </div>
<div><br></div><div>BinaryFile: pathname for ROI 1 </div><div>Operation: 0</div><div>etc. </div><div><br></div><div>BinaryFile: pathname for ROI 2 </div><div>Operation: 1</div><div>etc. </div><div><br></div><div>Binary File: pathname for first additional AND ROI</div>
<div>Operation: 1</div><div>etc. </div><div><br></div><div>Binary File: pathname for second additional AND ROI</div><div>Operation: 1</div><div>etc. </div><div><br></div><div>I do the same for all of the NOT ROIs. </div>
<div>
<br></div><div>When I do this, there are no tracts visible. Even if I take out all the NOT ROIs, there are still no tracts. I am able to see tracts only if the operations for the first four ROIs are set to zero (OR). I know that this is incorrect, because the AND operation must be used for those four ROIs. </div>
<div><br></div><div>Has anybody encountered a similar problem? </div><div>Thanks, </div><span><font color="#888888"><div><br></div><div>Deepa Krishnaswamy </div>
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