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not being able to break into the machine as such, i could only read what is in the DICOM header and therefore could be changed at the console. it says that the 'flip angle' is 180 degrees. s Peter Kochunov wrote: > No, I don't think so. That would have been true under "classic CPMG" > conditions, however, it won't work for siemens MSE sequence. Could you > check on the angle value of the refocusing pulse? If you haven't > changed it, it is probably still 120 degrees e.g. the value that is > the siemens template. > pk > > > ----- Original Message ----- From: "Scott Kolbe" > <[log in to unmask]> > To: <[log in to unmask]> > Sent: Monday, May 05, 2008 8:45 PM > Subject: Re: [FSL] multiecho T2 image acquisition question > > >> Peter, >> Do you think it is valid to use the CSF decay in the even echos to >> correct the odd echos? would the odd echo images be affected >> linearly? i am really hoping to be able to use the first echo to try >> and calculate myelin water fraction. >> s >> >> Peter Kochunov wrote: >>> 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 >>>> >> >> >> -- >> ======================== >> 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