After discussion with Steve S, and Mark J at FMRIB, we think that the most
likely reason for the difference is the scalefactors in the image headers.
If you used the DICOM conversion routine of SPM to convert Siemens Mosaic
DICOM data, then the images will all have different scalefactors in their
.hdr files. SPM uses these scalefactors, but FSL ignores them in data that
are not in the NIFTI-1 format. Instead, the FSL format assumes that all the
.img files are scaled equally. Because the images are in the SPM format,
rather than the FSL format, you would get blobs in SPM, but not FSL.
Best regards,
-John, Steve and Mark
> 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...!
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