[Mrtrix-discussion] Reverse phase encoding in Philips

[Luis Concha]

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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