Hi,
If you want to include STC then that is fine, but make sure you do it *after*
motion correction, not before. Otherwise you'll lock in incorrect spatial
locations into neighbouring timepoints (due to STC) and motion correction
will be unable to fix this. This is much worse than locking in temporal shifts
into the wrong voxels as the spatial changes can be up to 100% of the
mean intensity whereas temporal changes are normally only about 1%.
I know that some other people argue that STC (when it is done at all) should
be before motion correction but I strongly believe that this is wrong because
of the above argument, and stops motion correction removing some bigger
intensity changes, which is far worse than stopping STC from mopping up
some tiny changes.
All the best,
Mark
On 9 Dec 2011, at 00:13, David Grayson wrote:
I see, thanks for your response Mark. If it was imperative to include STC, though, say to compare with other data that had been processed that way, would it still be appropriate to apply it as a first step?
Thanks,
-David
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Mark Jenkinson
Sent: Thursday, December 08, 2011 12:30 AM
To: [log in to unmask]
Subject: Re: [FSL] pre-filtered to atlas transformed in one resampling step
Dear David,
Unless you do no smoothing it is unlikely that you would see a lot of benefit
from this kind of combination. We do try and reduce the number of steps as
it is, so you would, at most, get rid of one intermediate.
We also do not recommend slice-timing correction in general, and would
advocate using temporal derivatives in the GLM instead. Partly because of
this, our slice-timing-correction tool is not quite as well integrated, and I
do not think it would be possible with the existing tools to combine this as
a transformation that is applied simultaneously with the other spatial
transformations. So I'm sorry, but I think the answer here is that you cannot
do this, but for the reasons above I personally do not think it is important.
On 8 Dec 2011, at 01:17, David Grayson wrote:
There have been some posts on the listserv about this previously – what I’d like to do is apply all the feat pre-stats steps in one command, to achieve all the preprocessing in one resampling step, instead of multiple stages. It has been argued that this *may* improve power for later analyses, and I think I know how to implement this…
But my question is this: where then would I apply slice-timing correction? FSL’s standard procedure is to apply it right after mc and fieldmap-correction, but then I’m back to resampling my data more than once; is it equivalent to do slice-timing correction as the very first step instead?
