Hi Matt, thanks for your explanation. Can you give me an number on what
is a really low SNR?
cheers, Michael
Matt Glasser schrieb:
> Running eddy_correct on a big, merged, 4D volume (what I am guessing you saw
> that I suggested previously) accomplishes the same thing as eddy_correcting
> the individual datasets before averaging. The main reason to average before
> eddy correct (however after rigid body motion correction) is if your SNR is
> really low and eddy_correct is prone to failing.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Kochunov, Peter
> Sent: Saturday, September 20, 2008 7:22 PM
> To: [log in to unmask]
> Subject: Re: [FSL] eddy_correct before are after averaging
>
> Your physicist is giving you a sound advice. The most conservative way would
> be to process each set separately and merge them at the point of final
> results e.g. to average the FA images. However, this won't work if you're
> planning to do fiber tracking.
> pk
>
> ________________________________
>
> From: FSL - FMRIB's Software Library on behalf of Michael Scheel
> Sent: Sat 9/20/2008 6:48 PM
> To: [log in to unmask]
> Subject: Re: [FSL] eddy_correct before are after averaging
>
>
>
> Hi Markus, thanks for the answer. The reason I am asking was that my
> local physists told me it would be wise to do the eddy correction for
> every run seperately since the eddy currents could be very different
> from one run to the other.
> I used the suggestion that Matt gave in the forum archives and found
> them very convenient. Now my physists got me puzzled (as this is
> sometimes the case).
> So my question probably really is: Do the eddy currents change from run
> to run? Then the advice of running eddy current seperately would make sense.
>
> Thanks, Michael
>
> Markus Gschwind schrieb:
>> Hi!
>>
>> Concatenate them all together with fslmerge -t, then eddy_correct the
>> whole 4D file and then average them, after the eddy_correct.
>>
>> Hth, (there are some posts about this in the list, from e.g. Matt Glasser)
>> Markus
>>
>>
>> 2008/9/21 Michael Scheel <[log in to unmask]>:
>>> Hi fsl-expert,
>>>
>>> we have acquired the same dti sequence 3 times for averaging. I'd like to
>>> know if it is recommended to merge these 3 averages in one big file and
> then
>>> run eddy_correct OR first run eddy_correct on every dataset and then
> average
>>> them.
>>>
>>> Thanks, Michael
>>>
>>
>>
>
--
Michael Scheel
AG PD Dr. Stroehle
Klinik fuer Psychiatrie und Psychotheraphie
Charite - Campus Charite Mitte
[log in to unmask]
0176 - 20801852
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