Hi,
1. You should only have to run eddy_correct once.
2. I have run into this problem also, which is why you should verify the
output of eddy_correct (particularly for newer versions, older versions
didn't seem to make as many mistakes). In some cases, I have forgone using
eddy_correct on a dataset if the output is worse than the input.
3. use:
fslroi <big4d> <1staverage> 0 30
fslroi <big4d> <1staverage> 30 30
fslroi <big4d> <1staverage> 60 30
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Markus Gschwind
Sent: Wednesday, October 31, 2007 7:20 AM
To: [log in to unmask]
Subject: Re: [FSL] Averaging diffusion image
Hi Matt (again! ;-))
Thanks for your clarifications.
1. So you run edyycurrent several times over the same data. Is this
not a problem?
2. After I fslmerged the three 4D files to one and run eddycurent, I
still find that in the movie function of fslview there are still
motions visible (the same or even worse as in the non eddycorrected
file)
3. Could you please give me a hint how to use fslroi to re-separate
them (there are 3x30 volumes in this big volume).
Thanks a lot!
Cheers,
Markus
Quoting Matt Glasser <[log in to unmask]>:
> Hi,
>
> I usually run eddy_correct on the whole dataset before averaging by
> concatenating the 3 averages into a single big 4D file, with fslmerge, and
> running eddy_correct on that. Then split the 3 averages back out using
> fslroi and you can use fslmaths as you suggest below.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Markus Gschwind
> Sent: Tuesday, October 30, 2007 6:26 AM
> To: [log in to unmask]
> Subject: [FSL] Averaging diffusion image
>
> Hi Experts!
>
> I have 3 aquisitions of diffusion data D1, D2, D3 for one subject.
> I would like to take the average image for further processing.
> For that purpose I used the fslmaths -add and -div commands.
>
> My question:
> Actually I would have to correct for eddycurrent BEFORE averaging, is
> that true?
>
> Thanks a lot for help!
> Markus
>
>
> --
>
> Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
> 1 Michel-Servet - 1211 GENEVA - CH
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> http://labnic.unige.ch
>
--
Markus Gschwind, M.D.
Laboratory for Neurology and Imaging of Cognition
Dept of Neurosciences
University Medical Center (CMU)
1 Michel-Servet - 1211 GENEVA - CH
Tel 0041 (0) 22 379 5324
Fax 0041 (0) 22 379 5402
email: [log in to unmask]
http://labnic.unige.ch
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