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Bob, I think using a secondary effect (better coregistration) is not recommendable as this may also be brought about by a wrong setting (i.e., it is a likely, but not definite effect of the correct setting). I like James's idea (should have suggested that myself :) to figure things out for good in a setting where the ground truth is known. Good luck, Marko Bob Spunt wrote: > Hi Marko - thanks for the response. Would you say that a good way to > empirically evaluate the blip direction is to determine which value best > improves the registration of the unwarped EPI with the subject's > anatomical volume? I'm finding this to be the case for all my subjects > with blip = -1. > > Thanks again, > Bob > > > On Wed, Jan 9, 2013 at 12:51 AM, Marko Wilke > <[log in to unmask] > <mailto:[log in to unmask]>> wrote: > > Bob, > > while it naturally would be better to know the ground truth of what > blip dir is correct, I think what you do is a correct empirical > approach. Depending on how "optimized" an EPI sequence is, EPI > distortion is not as obvious as it used to be. As to how to detect > the correct blip direction, you usually also get some elongation in > ap-direction with EPI, the correction of which may be more obvious > than the attenuation of dropouts. I would also recommend subtracting > the uncorrected from the corrected image, so you can appreciate the > differences more directly. > > Hope this helps, > Marko > > Bob Spunt wrote: > > ... apologies for the re-post, still looking for advice ... > > Dear SPM experts, > > I am using the SPM fieldmap toolbox to compute VDMs/ unwarp EPIs > (oblique slice prescription, about -25 degrees) based on magnitude > images and a presubtracted phase image (collected using a > Siemens Trio > 3T). I have determined all protocol-specific parameters except > for the > blip direction. A colleague recommended I run it both ways (Blip > +1 and > Blip -1) and compare the resulting unwarped EPIs to determine > which is > the correct value. > > I have done this, however, the differences are not as clear as I had > expected to see. Attached is the most notable difference among > the two, > showing that Blip +1 seems to smear pixels posteriorly and thus > fills in > areas of dropout (I note again that these images are acquired with a > pretty steep slice angle). Blip -1 does the opposite (not > surprisingly); > moreover, the co-registration of the Blip -1 unwarped EPIs with the > hi-res anatomical (not pictured) is slightly (but noticeably) better > than with the Blip +1. > > Any advice on which is correct and/or tips on how to better > evaluate the > results? I of course want to make sure I'm using these maps > appropriately - thank you in advance for any help! > > Cheers, > Bob > > Inline image 1 > > > > On Fri, Dec 21, 2012 at 12:21 PM, Bob Spunt <[log in to unmask] > <mailto:[log in to unmask]> > <mailto:[log in to unmask] <mailto:[log in to unmask]>>> wrote: > > Dear SPM experts, > > I am using the SPM fieldmap toolbox to compute VDMs/ unwarp > EPIs > (oblique slice prescription, about -25 degrees) based on > magnitude > images and a presubtracted phase image (collected using a > Siemens > Trio 3T). I have determined all protocol-specific > parameters except > for the blip direction. A colleague recommended I run it > both ways > (Blip +1 and Blip -1) and compare the resulting unwarped > EPIs to > determine which is the correct value. > > I have done this, however, the differences are not as clear > as I had > expected to see. Attached is the most notable difference > among the > two, showing that Blip +1 seems to smear pixels posteriorly > and thus > fills in areas of dropout (I note again that these images are > acquired with a pretty steep slice angle). Blip -1 does the > opposite > (not surprisingly); moreover, the co-registration of the > Blip -1 > unwarped EPIs with the hi-res anatomical (not pictured) is > slightly > (but noticeably) better than with the Blip +1. > > Any advice on which is correct and/or tips on how to better > evaluate > the results? I of course want to make sure I'm using these maps > appropriately - thank you in advance for any help! > > Cheers, > Bob > > Inline image 1 > > > > -- > ______________________________________________________ > PD Dr. med. Marko Wilke > Facharzt für Kinder- und Jugendmedizin > Leiter, Experimentelle Pädiatrische Neurobildgebung > Universitäts-Kinderklinik > Abt. III (Neuropädiatrie) > > > Marko Wilke, MD, PhD > Pediatrician > Head, Experimental Pediatric Neuroimaging > University Children's Hospital > Dept. III (Pediatric Neurology) > > > Hoppe-Seyler-Str. 1 > D - 72076 Tübingen, Germany > Tel. +49 7071 29-83416 <tel:%2B49%207071%2029-83416> > Fax +49 7071 29-5473 <tel:%2B49%207071%2029-5473> > [log in to unmask] > <mailto:[log in to unmask]> > > http://www.medizin.uni-__tuebingen.de/kinder/epn/ > <http://www.medizin.uni-tuebingen.de/kinder/epn/> > ______________________________________________________ > > -- ____________________________________________________ PD Dr. med. Marko Wilke Facharzt für Kinder- und Jugendmedizin Leiter, Experimentelle Pädiatrische Neurobildgebung Universitäts-Kinderklinik Abt. III (Neuropädiatrie) Marko Wilke, MD, PhD Pediatrician Head, Experimental Pediatric Neuroimaging University Children's Hospital Dept. III (Pediatric Neurology) Hoppe-Seyler-Str. 1 D - 72076 Tübingen, Germany Tel. +49 7071 29-83416 Fax +49 7071 29-5473 [log in to unmask] http://www.medizin.uni-tuebingen.de/kinder/epn/ ____________________________________________________