Hi Cornelius,
Two possibilities spring to mind that might explain such strong
differences.
The first is that, given that the method of specification of timing
information is so different in SPM and FSL, there is the possibility that
the timing information was not quite correct for one of the methods.
The second is something that came up recently with a similar question on
the FSL list - it turned out that there was a huge amount of global
timepoint-to-timepoint intensity variation (which was an artefact induced
by the data format conversion process rather than a physics artefact).
Because it is common in SPM to use intensity normalisation, but in FSL
this is an option which is turned off by default, this explained the
difference in results.
Note that in either case it may well be informative to run MELODIC
(ICA-based model-free analysis) to see what's in the data.
Cheers, Steve.
On Fri, 3 Dec 2004, Cornelius Werner wrote:
> Hello list,
>
> just out of curiosity, I analyzed a fairly complex (and long) erfMRI
> experiment with a 3x3 factorial design with both SPM2 and FSL3.2b. I tried
> to keep everything as close to the other package as possible, i.e. I
> adjusted both smoothing kernels to 5mm, set the high pass filter to 128s,
> used gamma function + temp. derivative in FSL (standard delay) / canonical
> hrf + tdv in SPM2, entered identical onset vectors, specified identical
> contrasts and so on. I set the duration for my events to the actual 1.5
> seconds in both packages, as FSL doesn't allow 0-durations.
> Now one of the packages gave me "blobs" on a
> corrected-for-multiple-comparisons level of 0.05, where the other didn't
> show anything worth mentioning on a uncorrected p=0.001 level. Is that
> possible at all, given the similarity of the statistics? Has anyone
> experienced something similar? I am aware of the comparison done by
> Bianciardi et al (NeuroImage 2004), but differences were marginal at
> best...!
>
> Thanks for your help,
> Yours,
>
> --
> Cornelius Werner
> Institut fuer Medizin (IME)
> AG Kognitive Neurologie
> Forschungszentrum Juelich
> 52425 Juelich
> Germany
>
> Tel. +49-(0)2461-61-8609
>
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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