Hi,
No that's not safe in general - you should stick to the same order
that FEAT applies these things (it's the order that they appear in the
GUI and the log files).
In particular, it doesn't make sense to run BET first as this will
create artificial intensity boundaries which will confuse (e.g.) the
motion correction.
Cheers.
On 2 Jun 2008, at 22:24, Todd Penney wrote:
> Hi there,
>
> I just had a question regarding the order of preprocessing steps in
> fMRI. Is it safe to perform brain voxel extraction (BET) before
> slice timing, motion correction, spatial smoothing, etc
> preprocessing steps are done? In the preprocessing steps of fMRI
> FEAT, is BET done before any other preprocessing step?
>
> I've preprocessed some of my fMRI data using the following order of
> steps:
>
> 1. BET(FSL)
> 2. Slice timing correction (SPM)
> 3. Motion correction (SPM)
> 4. Spatial smoothing (SPM)
> 5. Temporal filtering (FSL)
>
> Does anyone see a potential problem doing the preprocessing in this
> order? By the way, the fMRI scans were acquired in an interleaved
> fashion, so slice timing is done before motion correction in this
> case.
>
> Thank you!
>
> Todd Penney
>
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