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<div>Hi Donald,</div>
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<div>Thanks for the tip. I checked the b values, and the b=0 are indeed listed as b=5 in the subjects that failed to be processed, and editing the encoding file solves the issue. <br>
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David</div>
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Le 29 janv. 2013 à 03:10, "Donald Tournier" <<a href="mailto:d.tournier@brain.org.au">d.tournier@brain.org.au</a>> a écrit :<br>
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<div>Hi David,
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<div>I'm not sure what might be causing this, but it might be due to the b=0 images not being specified as b=0 in the DW encoding file. MRtrix basically assumes that the data consist of a single-shell HARDI with some b=0 images in it, and assumes that any volumes
with a non-zero b-value are part of the HARDI shell. So if the b=0 images are actually specified as some low non-zero value, this will mess things up. Note this only affects the CSD, not the DTI fit.</div>
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<div>To fix this (assuming that this is indeed the problem), you need to edit the encoding. This will depend on whether you're using the DICOM or NIfTI version of the data. Assuming DICOM, then export the encoding file using the "mrinfo <dataset> -grad encoding.b"
command. If using the NIfTI data, then I assume you've already come up with a way of creating that file. You'll then need to edit the file, and identify the b=0 volumes. The file is a 4-column matrix of values, the last column in the b-value. If the b-zeros
are not zero, then set them to zero, save, and use that new file for the estimate-response and csdeconv commands, using the -grad option. If they were already zero, then the problem is elsewhere and I'll have to download the data to see where the problem might
be...</div>
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<div>Hope this fixes it. Let me know how you go.</div>
<div>Cheers,</div>
<div><br>
Donald.</div>
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<div class="gmail_quote">On 26 January 2013 00:25, David Coynel <span dir="ltr"><<a href="mailto:david.coynel@unibas.ch" target="_blank">david.coynel@unibas.ch</a>></span> wrote:<br>
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<div style="word-wrap:break-word">Hi, and thanks for this nice software,
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<div>I'm having a problem when trying to do whole-brain tractography out of CSD data. The DWI data that I'm testing are those released by the f1000 connectome (<a href="http://fcon_1000.projects.nitrc.org/indi/enhanced/download.html" target="_blank">http://fcon_1000.projects.nitrc.org/indi/enhanced/download.html</a>),
with 137 directions and b=1500m/s2. I followed the step-by-step procedure from the website, starting from dicom images. Although the response function estimated with an order of 8 looks totally normal, the FOD I obtain don't look perfect at all, and generate
the type of whole brain tracking as shown on the attached picture (tracking parameters are all default). </div>
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<div>I would appreciate if you could point me to a possible explanation for that.</div>
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<div>Thanks,<br>
David </div>
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<div><screenshot-0000.png></div>
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-- <br>
<font color="#ff6600" size="1"><b>Dr Jacques-Donald Tournier<br>
</b></font>
<div><font color="#ff6600" size="1">Research Fellow</font></div>
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<div><font size="1">The Florey Institute of Neuroscience and Mental Health</font></div>
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