Hi Peter,<div><br></div><div>I assume you supplied the gradient directions manually, rather than having MRtrix read them straight from the DICOM headers? If not, then that would be a bug that I'd need to fix. But otherwise, yes, there is no simple way to change the sign of the gradients on the command line, but it should be pretty straightforward to load the file in matlab and do it there, or write a tiny python script to do it. </div>
<div><br></div><div>By the way, if you do supply the directions manually, be aware that the directions in MRtrix are assumed to be provided with respect to real-world/scanner coordinates, not the image axes as is usually the case for FSL and others. This will cause issues if your images are not acquired as straight axials. </div>
<div><br></div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br><br><div class="gmail_quote">On 31 July 2012 22:58, Peter Neher <span dir="ltr"><<a href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all,<br>
<br>
I am having some trouble with my tensor reconstruction. There seems to be a sign issue with the z-component of the gradients directions. Is it possible to correct this with any command line option or do I have to directly change the sign in the gradient encoding file?<br>
<br>
Best<br>
Peter<br>
<br>
-- <br>
Dipl.-Inform. Peter Neher<br>
German Cancer Research Centre<br>
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)<br>
Division of Medical and Biological Informatics<br>
Im Neuenheimer Feld 280, D-69120 Heidelberg<br>
<br>
Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345<br>
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