My understanding is that you don't have any NOT roi. Operation 1 is for AND ROIs. So no fibers pass in all those ROIs<div><br></div><div>ROI Operation: 0=OR, 1=AND, 3=NOT, 4=Cut0, 5=Cut1, 6=AndClr, 7=NotClr, 8=CutClr0, 9=CutClr1</div>
<div><br></div><div>Dorian<br><br><div class="gmail_quote">2013/1/30 Deepa Krishnaswamy <span dir="ltr"><<a href="mailto:deepa.krishnaswamy1@gmail.com" target="_blank">deepa.krishnaswamy1@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>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 class="HOEnZb"><font color="#888888"><div><br></div><div>Deepa Krishnaswamy </div>
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