Hello All,
I’m using a GE 3T scanner and my interleave sequence is 1,3,5,...2,4,6,... (not sure if it is bottom up or top down) and fsl's is 0,2,4,6...1,3,5,.. So apparently, these two are identical because of the zero? (Q1) Anyways, I ran FSL’s (0,2,4,6...1,3,5,..) and (regular up) and there were differences but not very obvious. I also ran my own slice timing file
1
3
5
...
23
2
4
6
...
22
And the results were drastically different from the previous two. Actually, it seemed like it was haven’t problems fitting the model. So, shouldn’t this file have given similar results to FSL’s (0,2,4,6...1,3,5,..)? (Q2)
After reading some more of the threads on slice timing. It seems like this is scanner dependent and also total slice # dependent, for instance, 23 slices vs 24, may change the slice order.
Overall, if someone doesn’t catch these differences (in my case by accident). Then the slice timing can throw off their results. My next step is to run NO slice timing as it may be doing more harm than good, according to Steve Smith’s thread back in 2003. http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind03&L=FSL&P=R14896&I=-3 , which is copied below.
BTW, I should point out that slice-timing-correction is not in general necessarily a helpful thing to do; the slight loss of temporal information (because of the necessary interpolation used to achieve the time shift) may outweigh the advantage of having perfect "slice timing". Furthermore, it is not very satisfying to have to do the timing correction as a separate stage from the motion correction; integrating these is something which we are working on for the future.
But I don’t know how relevant this is now in 2007. Would this be proper to do? (Q3)
Finally, I would like to know exactly how the slice-timing correction works. I guess my big question is, how does it interpolate the data? Specifically, is it just shifting the model timings, or is it changing the intensity values of the data somehow? If the latter, what are the intensity changes based on? (Q4)
Thanks
Nasser
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