Hi Deepa,<div><br></div><div>Before using the automated method introduced by the Yajing's paper, please perform the manual-based analysis (paper attached) to make sure your data are ready for tractography.</div><div><br>
</div><div>The most common problem is, as you indicated, the sign of the fiber vectors. If you are using Siemens DICOM (MOSAIC), I recommend you to obtain gradient vector information from the header using the "Get gradient from DICOM file header" function. If you use this information, no "flipping" is necessary. If the fiber angles are correct, you should find many streamlines that connect the brainstem and the motor cortex.</div>
<div><br></div><div>Susumu<br><br><div class="gmail_quote">On Wed, Feb 13, 2013 at 7:09 PM, Deepa Krishnaswamy <span dir="ltr"><<a href="mailto:deepa.krishnaswamy1@gmail.com" target="_blank">deepa.krishnaswamy1@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>Yes I do understand that you would expect a lot less fibers. I am trying to recreate a similar looking CST as is shown in the paper 'Atlas-guided tract reconstruction for automated and comprehensive examination of the white matter anatomy.' I have been using the sample Siemens DICOM dataset, FA of 0.2 and an angle constraint of 40 degrees, as these were values given in the paper. This does not yield many fibers at all; in fact most do not reach the motor cortex. I've tried experimenting with the FA threshold and the angle constraint, but this does not seem to yield any better fibers. Is there anything else I can modify to yield more CST fibers? The only other issue I have thought of is that the flipping of the eigenvectors was incorrect, but I am pretty sure that there must be a Y and Z flip. </div>
<div>Thanks, </div>
<div><br></div><div>Deepa <br><br><div class="gmail_quote">On Thu, Feb 7, 2013 at 10:48 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 Deepa,<div><br></div><div>if you specify the second ROI with "1", the fibers have to penetrate both ROIs. So usually, you expect much less fibers.</div><span><font color="#888888"><div><br></div>
</font></span><div><span><font color="#888888">Susumu</font></span><div><div><br><br><div class="gmail_quote">
On Thu, Feb 7, 2013 at 1:21 PM, Deepa Krishnaswamy <span dir="ltr"><<a href="mailto:deepa.krishnaswamy1@gmail.com" target="_blank">deepa.krishnaswamy1@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>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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