Dear Jesper & others,
Thank you very much for our latest toy which I have been playing with
today. Just a few questions though if I may:
1) Is unwarping compatible with slice timing correction? And if so
should the slice timing correction then be done prior to realignment
despite the exact ordering of slice acquisitions?
I appreciate that this is a controversial issue
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind9905&L=spm&P=R11823
but wondered if unwarping might necessitate a particular ordering.
2) In the case of an interleaved acquisition presumably things
get horribly complicated such that you are effectively looking
at yourself through strips of different fairground mirrors each
with some sort of built in reflection delay. Is unwarping still
potentially applicable or useful?
Is it not the case for example that the deformation fields need to
have some sort of 'spatial smoothness symmetry'? (not an official term!)
3) To further complicate matters is there any future scope
for implementing something like John's spin history correction
in the resampling process or is it redundant under the circumstances?
4)
>afflicted by a particular problem. If there is little movement in your
>data to begin with this method will do you no good.
No good is OK but might it do any harm?
Or more specifically where one is dealing with a group of subject, some
with poor and others with good motion, should one perform unwarping
on all subjects for the sake of methodological consistency?
5)
>if there is appreciable movement in your data (>1mm or >1deg) it will
>remove some of that unwanted variance.
A lot of people would consider motion over a 1mm to be unacceptable
particularly as a jerk. Are you suggesting that this need not be the
case anymore if one unwarps? Is the estimated signal recovery so great
as to potentially overcome the other problems (e.g. intra volume motion
ghost motion, spin history effects etc etc...)
Any guidelines?
6)
>The method attempts to minimize total (across the image volume) variance
>in the data set. It should be realised that while (for small movements)
>a rather limited portion of the total variance is removed, the
>susceptibility-by-movement interaction effects are quite localized to
>"problem" areas. Hence, for a subset of voxels in e.g. frontal-medial
>and orbitofronal cortices and parts of the temporal lobes the reduction
>can be quite dramatic (>90%).
Is there then a recommended upper limit in terms of movement
beyond which unwarping is no longer helpful?
I think 6 is enough for starters!
Very much appreciated,
Afraim
---------
Dr A Salek-Haddadi
Clinical Research Fellow
Institute of Neurology
