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/
____________________________________________________
|