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
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