[Mrtrix-discussion] Reverse phase encoding in Philips

Dorian P. alb.net at gmail.com
Mon Jan 13 08:25:17 PST 2014

Great help. Thank you Dr. Concha.

2014/1/13 Luis Concha <lconcha at unam.mx>

> Hello.
> A recent post (
> http://www.nitrc.org/pipermail/mrtrix-discussion/2014-January/000860.html)
> 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:
> 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.
> 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.
> 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.
> Remarks:
> * I have only tried this on a 3T Achieva TX, so I do not know if it will
> work for other scanners/configurations.
> * 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!
> * hat tip to  Bernd Foerster (Philips) for teaching me how to do this.
> * If you have an easier/better way to do this, let me know!
> Cheers.
> Dr. Luis Concha
> Instituto de Neurobiología
> Laboratorio C-13
> UNAM, Campus Juriquilla
> Boulervard Juriquilla 3001
> Juriquilla, Querétaro.
> C.P. 76230
> México
> Tel (442) 2 38 10 54
> Fax (442) 2 38 10 46
> http://personal.inb.unam.mx/lconcha/
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