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Thanks very much for your thoughtful reply Jonathan, I will follow some of these avenues you've suggested. I have indeed checked realignment, and these analyses are in native space so normalisation is a non-issue. Best, Graeme On Tue, Jun 1, 2010 at 6:51 AM, Jonathan Peelle <[log in to unmask]> wrote: > Hi Graeme > > > I thought I'd ask the collective wisdom and experience of the SPM list if > > they've ever seen out of brain clusters like those in the attached image. > > These are first-level individual subject SPMs at a FDR 0.05 10 voxel > > threshold. A number of subjects are showing highly significant clusters > way > > outside the skull. Some are in the bone, but many are multiple mm away > from > > any tissues, and I wonder what might be causing them? Could residual > motion > > in anyway be responsible? > > Having signal outside the brain isn't all that unusual, and in fact, > because the variance is low, these can even be quite significant. > However, generally these are masked out by the proportional > thresholding SPM does by default. So the first thing I would check is > the mask.img in the 1st level stats directory, which shows all the > voxels that SPM included in the analysis. Generally this looks > something like a brain mask, and if not, it would be good to figure > out why. > > (Of course, your initial thoughts are good as well---checking that > realignment and normalization worked properly are the first things I > would check, I'm just assuming from what you've said you've checked > that already.) > > > I'm concerned it is some kind of scanner noise, and it seems to be > appearing > > more frequently in my recent scans, and need to decide if we should > suspend > > scanning. > > To evaluate potential scanner noise I would recommend some sort of > timeseries analysis that gives an indication of scan-to-scan variance. > I've had good luck with tsdiffana: > > http://imaging.mrc-cbu.cam.ac.uk/imaging/DataDiagnostics > > but there are several other options out there, which you may find by > digging into the list a bit. If you're worried about scanner noise it > may also be worth talking to physicists about phantom results, if > those are available... (e.g. Friedman & Glover (2006), > http://dx.doi.org/10.1002/jmri.20583). > > Good luck! > > Jonathan >