Hello Helmut,
with regard to some of your fieldmap questions... ;)
> - apply VDM and later on realign
> - realign & unwarp and load the vdm file during that step
>
> Has anyone tried to compare these two options?
I have not, but do not see why the former option would appeal to you
more. In fact, realign & unwarp should be called realign & unwarp &
unwarp (which was probably considered too bulky ;) as it aims to correct
for motion, motion*B0 interaction, and EPI distortions. The latter is
only done if a fieldmap is provided. I do not think that unwarping the
EPIs prior to simple realignment is superior, but I must admit I have
not checked this (but have been using the latter option for years now
adn am quite happy with the results).
> I would like to enter the realignment parameters as regressors on single-subject level. Based on previous threads I'm a little sceptic about "realign & unwarp" as it seems that unwarp is redundant when adding the movement regressors. Any ideas?
I think I am guilty of starting some of these threads. Jesper once
mentioned it would be overkill to do both, which I would tend to agree
with (again without having looked into this specifically). As an
alternative, you could check out the motion fingerprint approach (PMID:
22036679) which tries to model motion effects on the data and may
therefore be more independent from realign & unwarp than the realignment
parameters.
With regard to the blipdir question in the next mail, I think there may
be a good reason for it but if my memory serves me right, this setting
changed in the last couple of years with an spm upgrade. I would
therefore recommend to simply generate a vdm and apply it to one of your
EPIs from within the fieldmap gui, using both settings. It should be
pretty apparent which one is correct :)
Cheers,
Marko
--
____________________________________________________
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/
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