> Date: Tue, 28 May 2013 10:17:59 +0200
> From:
[log in to unmask]> Subject: Re: [FSL] Combine topup and eddy to perform DTI correction
> To:
[log in to unmask]>
> Dear Paul,
>
> this looks exactly right. Please let me know how it goes.
>
> Good luck Jesper
>
> On 27 May 2013, at 17:43, Paul Chou wrote:
>
> > Dear all FSL experts
> >
> > Thanks for Jesper to provide such excellent correction tool for DTI dataset, currently I acquire the blip up blip down DTI dataset and try to use TOPUP and EDDY to perform DTI correction. I have some setting problems and ask for help to check the usage of the tool correct or not:
> >
> > My dataset as acquired like follows:
> >
> > PE+ = { b0 b0 b0 dwi (with 30 directions)}
> > PE- = { b0 b0 b0 dwi (with 30 directions)}
> >
> > I make a topup --imain file like
> > tp = { b0-PE+ b0-PE+ b0-PE+ b0-PE- b0-PE- b0-PE- }
> >
> > and acqparams.txt file like follows and run topup
> >
> > 0 1 0 0.062
> > 0 1 0 0.062
> > 0 1 0 0.062
> > 0 -1 0 0.062
> > 0 -1 0 0.062
> > 0 -1 0 0.062
> >
> > The output of TOPUP looks great and non I want to use TOPUP together with EDDY, I make a "total" dataset for eddy like follows:
> >
> > ed = { b0-PE+ b0-PE+ b0-PE+ dwi-PE+ (with 30 directions) b0-PE- b0-PE- b0-PE- dwi-PE- (with 30 directions)}
> >
> > In order to incorporate EDDY with TOPUP, I use the same acqparams.txt (which used in TOPUP) with EDDY. Is it right to use the same acqparams.txt for EDDY? I aslo set the index file like follows:
> >
> > index.txt = {1 1 1.....(with 30's 1) and 4 4 4.... (with 30's 4) }
> >
> > Is the overall procedure list as above valid for my own dataset? Thanks for your kindly help.
> >
> > Best
> >
> > Paul
> >
