if you have access to the IDEA, there is a number of things you can do to make this sequence more stable. Replacing the refocusing pulses and playing with the crasher gradients to move the STE away from the echo should make this sequence more "scientific"
pk
________________________________
From: FSL - FMRIB's Software Library on behalf of Scott Kolbe
Sent: Mon 5/5/2008 9:52 PM
To: [log in to unmask]
Subject: Re: [FSL] multiecho T2 image acquisition question
Thanks for all the help. i am going to follow this up with Siemens.
s
Kochunov, Peter wrote:
Well, at least you've used the proper refocusing flip angle.
pk
________________________________
From: FSL - FMRIB's Software Library on behalf of Scott Kolbe
Sent: Mon 5/5/2008 9:10 PM
To: [log in to unmask]
Subject: Re: [FSL] multiecho T2 image acquisition question
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]> <mailto:[log in to unmask]>
To: <[log in to unmask]> <mailto:[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]> <mailto:[log in to unmask]>
To: <[log in to unmask]> <mailto:[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]> <mailto:[log in to unmask]>
To: <[log in to unmask]> <mailto:[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]> <mailto:[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
--
========================
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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