<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>Hi all, </div><div><br></div><div>I have a query regarding the coordinate frame used by mrtrix.</div><div><br></div><div>I have a DTI dataset acquired by a 1.5 Tesla GE SIGNA NVi scanner. </div><div>According to the manufacturer the scanner uses a right-handed coordinate system, that is:</div><div><br></div><div>dimension<span class="Apple-tab-span" style="white-space:pre"> </span>description</div><div>0 (x)<span class="Apple-tab-span" style="white-space:pre"> </span>increasing from right to left</div><div>1 (y)<span class="Apple-tab-span" style="white-space:pre"> </span>increasing from posterior to anterior</div><div>2 (z)<span class="Apple-tab-span" style="white-space:pre"> </span>increasing from inferior to superior</div><div><br></div><div>I have uploaded the an image showing the details of the coordinate system. </div><div>Tractography carried out with mrtrix and the original gradient table (provided by GE) looks correct. </div><div><br></div><div>From the description of the coordinate system used by mrtrix (<a href="http://www.brain.org.au/software/mrtrix/general/overview.html#axes">http://www.brain.org.au/software/mrtrix/general/overview.html#axes</a>) I understand that mrtrix uses a different convention and therefore I think I should swap the X axis.</div><div>However, if I do swap X, the results of tractography are not clearly not plausible. </div><div><br></div><div>I was wondering if you can shed a light on this. </div><div>Many thanks again for your help.</div><div><br></div><div>Francesco</div></div><div><br></div><div><img id="4b2c57a9-17d9-4427-a9ae-af895c15e644" height="211" width="298" apple-width="yes" apple-height="yes" src="cid:A77538F4-9540-41A5-A3E6-12B9F5F08C88@bc.iop.kcl.ac.uk"></div><div><br></div><br><div apple-content-edited="true">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="orphans: 2; text-align: -webkit-auto; text-indent: 0px; widows: 2; -webkit-text-decorations-in-effect: none; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="orphans: 2; text-indent: 0px; widows: 2; -webkit-text-decorations-in-effect: none; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="orphans: 2; text-indent: 0px; widows: 2; -webkit-text-decorations-in-effect: none; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="orphans: 2; text-indent: 0px; widows: 2; -webkit-text-decorations-in-effect: none; "><div style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dr Francesco Carletti - Neuroradiologist<br>Wellcome Research Training Fellow</div><div style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br>King's College London<br>King's Health Partners</div><div style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Department of Psychosis Studies</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Department of Neuroimaging, Center for Neuroimaging Sciences</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Institute of Psychiatry</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Box PO67<br>London SE5 8AF, UK<br><br>tel: +44 (0)20 7848 0049<br>fax: +44 (0)20 7848 0976<br>email: <a href="mailto:francesco.carletti@kcl.ac.uk">francesco.carletti@kcl.ac.uk</a></div></span></div></span></div></span></div></span></div></div>
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