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Dear Helmut, Marko, Mike, Dennis, Thank you all for your response. I realized that I had to reslice the data at some point. Once I resliced the data, my statistics works fine. Thanks Helmut for providing the detailed explanation with respect to why reslicing is necessary. I am still experimenting with slice timing and where to place it. I went through mindhive and I am right now redoing my analysis with slice timing first. We are having interleaved acquisition. The slice order is [1:2:31 2:2:31]. So the center slice is 31 (according to the order it is acquired). However, I am not sure what to provide for the reference slice in slice timing. I read through some of the previous thread addressing the same issue and I think everyone suggest to use 31 as the reference slice. And in the statistics we should set microtime resolution to 31 and microtime onset to 16 (so that the regressor is set to the middle slice). Am I correct here? SPM advices to set the microtime resolution to its default value 16, so I want to make sure I am doing it right. Thank you once again. Balu On Fri, Oct 18, 2013 at 2:03 PM, H. Nebl <[log in to unmask]>wrote: > Dear Balu, > > > when conducting single-subject analyses the data has to be resliced at > some point (this is done during normalisation step otherwise). As Marko > stated, during "Realignment: Estimate" the headers of the images are > adjusted, but the data itself is not resliced (motion parameters are not > applied to the data). This means one voxel in volume 1 does not correspond > to the same voxel in volume 2. However, during slice timing motion > parameters are NOT applied to the data either (nor during smoothing). To > solve this issue you have to reslice your data somewhere. Otherwise you get > some error similar to yours when trying to run single-subject models. The > same error might occur during group statistics if data from different > subjects weren't normalised the same way (something like different bounding > box) or if you try to run group statistics on data in native space. > > Concerning the order of slice timing and realignment see > http://mindhive.mit.edu/node/109 for more information. With interleaved > acquisiton scheme it is probably better to start with slice timing [if you > expect rather large motion between subsequent scans then slice timing > introduces some error indeed, but in this case your data is rather > problematic anyway. Then your data suffers from motion artefacts and you > should probably avoid slice timing completely or at least, replace affected > volumes - otherwise you transfer artefacts from an affected volume to > neighbouring unaffected volumes]. So for analyses in native space go with > ST -> "Realignment: Estimate & Write", when using normalisation go with ST > -> "Realignment: Estimate". > > If you don't want to start with slice timing, then you HAVE to use > "Realignment: Estimate & Write" as far as I can see, even if your > preprocessing pipeline includes a normalisation step. Otherwise you correct > temporally within your original slices, which is exactly not what you want > when starting with realignment. You can try yourself if you "realign > manually" via the Display function and flip one volume along y for example > (resize(y) = -1). After slice timing the temporally neighbouring volumes > should have different values then, depending on whether you use the > original data or the time series with the flipped volume. But they do not. > > > Best, > > Helmut > > -- Balu Krishnan,