<div dir="ltr">Great help. Thank you Dr. Concha.</div><div class="gmail_extra"><br><br><div class="gmail_quote">2014/1/13 Luis Concha <span dir="ltr"><<a href="mailto:lconcha@unam.mx" target="_blank">lconcha@unam.mx</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Hello.<br><br></div>A recent post (<a href="http://www.nitrc.org/pipermail/mrtrix-discussion/2014-January/000860.html" target="_blank">http://www.nitrc.org/pipermail/mrtrix-discussion/2014-January/000860.html</a>) raised the issue of improving image registration through the minimization of geometric inhomogeneities by use of a phase-reversed image, eddy and topup (fsl's tools). Robert Smith kindly provided instructions for Siemens, and here are the corresponding for Philips:<br>
<br></div>1. Create your DWI protocol according to your needs. Make sure that the TR and TE are set to User Defined, so that they are not modified in step 2.<br></div>2. Copy that DWI sequence and in the Contrast tab, set the number of diffusion gradient directions to one. You will also get a b=0 image, which is what will be used.<br>
</div>3. In the Geometry tab, you should normally see AP as the fold-over direction (i.e., phase encoding is done AP). Just below it, the setting "fat shift direction" (or something like that, I cannot remember right now) should read either A or P. Change it to whatever the opposite is. This is what controls the phase reversal, and you only need one image to do this.<br>
<div><div><div><div><br></div><div>Remarks: <br>* I have only tried this on a 3T Achieva TX, so I do not know if it will work for other scanners/configurations.<br></div><div>* fsl's topup and eddy are extremely flexibe and thus hard to use for the first time, but with a little patience it should work. Follow the tutorial on these tools. Attached is a script I made for my data that may or may not work for you, but it includes pointers to troublesome details of eddy and topup. Note that some things are hard-coded for my needs!<br>
</div><div>* hat tip to Bernd Foerster (Philips) for teaching me how to do this.<br></div><div>* If you have an easier/better way to do this, let me know!<br></div><div><br></div><div>Cheers.<br></div><div><br clear="all">
<div><div><div dir="ltr">Dr. Luis Concha<br>Instituto de Neurobiología<br>Laboratorio C-13<br>UNAM, Campus Juriquilla<br>Boulervard Juriquilla 3001<br>Juriquilla, Querétaro.<br>C.P. 76230<br>México<br>Tel <a href="tel:%28442%29%202%2038%2010%2054" value="+14422381054" target="_blank">(442) 2 38 10 54</a><br>
Fax <a href="tel:%28442%29%202%2038%2010%2046" value="+14422381046" target="_blank">(442) 2 38 10 46</a><br><a href="http://personal.inb.unam.mx/lconcha/" target="_blank">http://personal.inb.unam.mx/lconcha/</a><br></div>
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