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
>
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