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Hi Mark, thanks a lot for your answer! In the meantime I calculated the difference between the flirt_applyxfm output and the applyxfm4D output, using fslmaths. The resulting difference has a mean intensity that corresponds to about 2 % of the mean intensitity of the original time series (I looked that up in fslview). I also noticed 2 other things: first, the flirt_applyxfm output looks a bit smoother than the applyxfm4d output, and second, the applyxfm4d procedure takes much longer than the flirt_applyxfm operation. The 2 % seem a rather high difference to me, so I now have to decide which of the two possibilities I choose... I have the intuition that the applyxfm4D might be the more exact one because it takes longer to calculate:-)... What would you suggest? Cheers, Lea Am 08.10.2007 18:46 Uhr schrieb "Mark Jenkinson" unter <[log in to unmask]>: > Hi, > > That's right. > There shouldn't be any real difference (although sometimes there > are very slight numerical differences, but nothing big) if you only > want to apply a single transformation to all the volumes in a 4D series. > > All the best, > Mark > > > On 8 Oct 2007, at 10:45, Lea Krugel wrote: > >> Dear FSL people, >> >> I'd like to know whether "applyxfm4D" with only one transformation >> matrix >> for all the volumes of a functional data set leads to somehow >> different >> results than flirt in combination with "applyxfm" and "init". >> I'm asking because I used "applyxfm" for my functional data and >> FEAT has no >> problems in recognising the correct number of time points, so I >> guess the >> "applyxfm" command works fine here, also for functional data. My >> understanding of "applyxfm4D" would then be that it is the right >> tool when >> applying more than one transformation matrix to the data, but with >> only one >> there is no difference between "applyxfm" and "applyxfm4D". Is that >> right or >> might there be problems with my output in later analysis steps? >> >> Thanks a lot, >> Lea >> >> >> >> ------------------------------------------- >> Lea Krugel >> >> Max Planck Institute for Human Development >> Neurocognition of decision making >> Lentzeallee 94 >> 14195 Berlin >> Tel.: +49-30-82406618 >> Fax: +49-30-82406616 >> email: [log in to unmask] ------------------------------------------- Lea Krugel Max Planck Institute for Human Development Neurocognition of decision making Lentzeallee 94 14195 Berlin Tel.: +49-30-82406618 Fax: +49-30-82406616 email: [log in to unmask]