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Depends on the sequence some deal with that better than others. The stimulated echo contributes to the second echo and then it is being refocused with the main echo, the contributions from the stimulated echos from the third, and later pulses is going to be smaller since magnetization is going to decay, but it can produce an odd-even echo differences you observe. And yes, siemens MSE sequence isn't particularly good as far as dealing with stimulated echo. For this sort of sequence, I think the most robust processing will be to discard the first echo and just fit the rest of the data. pk ----- Original Message ----- From: "Scott Kolbe" <[log in to unmask]> To: <[log in to unmask]> Sent: Monday, May 05, 2008 8:22 PM Subject: Re: [FSL] multiecho T2 image acquisition question > Thanks Peter, Steve and David for the insights. > One follow-up question, would the stimulated echo effect be expected to > dimish in later odd echos? Here is are the intensity values for a voxel in > ventriclar CSF which one wouldn't expect to vary much in 132ms: > 1333 > 1567 > 1487 > 1509 > 1490 > 1479 > 1473 > 1453 > > As you can see, the odd/even difference is apparent but it is small > compared to the difference between the first and second echos. Is it > possible that the first refocussing pulse could vary in accuracy to later > ones or that the spoiler gradients could vary in magnitude? This sequence > was acquired on a 3T Trio TIM if anyone has experience with this kind of > imaging on this particular machine. > > Thanks again for your time, > Scott > > > Peter Kochunov wrote: >> Scott, >> To be very technical, it is the stimulated echo produced by your second >> refocusing pulse, due to less then perfect refocusing, that adds the >> extra signal to the even echoes. So, one way to deal with this to fit >> your data based on even and then odd echoes and average the results. >> There are ways of reducing your stimulated echo, first make sure that you >> do use 180 degree pulses for refocusing. You can try changing the >> refocusing pulse for an adiabatic. And if you have access to the pulse >> sequence you can up the magnitude of the crusher gradients, or even make >> them asymmetric. >> pk >> >> ----- Original Message ----- From: "David Lythgoe" >> <[log in to unmask]> >> To: <[log in to unmask]> >> Sent: Monday, May 05, 2008 8:29 AM >> Subject: Re: [FSL] multiecho T2 image acquisition question >> >> >>> Hi Scott, >>> >>> In multiple spin echoes, errors in the flip angle for the refocusing >>> pulses >>> can lead to reduced signal on odd echoes. These are compensated for to >>> some >>> extent on even echoes. >>> Even if you get perfect 180 pulses at the centre of your image slices, >>> the >>> slice profile won't be perfectly square, and you will have reduced flip >>> angle further from the centre of the slice. >>> Do all your even echoes have higher signal than expected? >>> Also, remember the T2 for CSF is quite long. >>> >>> >>> Dave >>> >>> >>> >>> On 5/5/08 10:05, "Scott Kolbe" <[log in to unmask]> wrote: >>> >>>> Dear FSL list >>>> this is a question not directly related to FSL but I am a bit lost for >>>> an alternative place to ask for advice. I have acquired multiecho T2 >>>> images to study relaxation times in a patient group. i found that for >>>> the first echo image (13ms) the CSF signal is actually darker than in >>>> the second echo image (26ms) by about 10%. i have acquired 8 echos and >>>> for the final echo image (132ms), the CSF signal is only 3% darker than >>>> for the second echo. >>>> My question is, does anyone have any idea why the first echo would be >>>> darker than the second. i had presumed that the earlier the echo is >>>> collected, the more signal there is. is that true in practice? >>>> >>>> thanks in advance >>>> Scott >>>> >>>> ======================== >>>> Scott Kolbe >>>> Postgraduate Student >>>> Neuroimaging Group >>>> Howard Florey Institute & >>>> Centre for Neuroscience >>>> University of Melbourne >>>> VIC, Australia, 3010. >>>> >>>> ph: +61 3 8344 1887 >>>> email: [log in to unmask] >>>> website: http://www.neuroimaging.org.au/index.php?id=383 >>> > > > -- > ======================== > Scott Kolbe > Postgraduate Student > Neuroimaging Group > Howard Florey Institute & > Centre for Neuroscience > University of Melbourne > VIC, Australia, 3010. > > ph: +61 3 8344 1887 > email: [log in to unmask] > website: http://www.neuroimaging.org.au/index.php?id=383 >