Hi again,
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> Ok the relation between index acqp and --inmain is quite clear in the documentation. What I miss is that it should be coherent between topup and eddy. If I do well understand, this mean that acquisition parameter (-acqp) should be the same one use in topup and eddy.
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> for instance I have 6 B0 in blip_up and blip_down so. So I merged the 12 B0 in 4D_dti file and run :
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> topup --imain=4D_dti.nii.gz --datain=acqp.txt --config=b02b0.cnf --out=4D_dti_topup
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>
> and the acqp.txt contain
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> 0 1 0 0.0909
> 0 1 0 0.0909
> 0 1 0 0.0909
> 0 1 0 0.0909
> 0 1 0 0.0909
> 0 1 0 0.0909
> 0 -1 0 0.0909
> 0 -1 0 0.0909
> 0 -1 0 0.0909
> 0 -1 0 0.0909
> 0 -1 0 0.0909
> 0 -1 0 0.0909
>
>
> but then when I ran eddy I made an other acqp.txt with only 2 lines
> 0 1 0 0.0909
> 0 -1 0 0.0909
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>
> So the 2 acqp.txt paramters and ok for each fonction separatly. but when you run eddy with the -topup option it is then not ok is it ?
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> So I keep the first acqp.txt for eddy (the one use for topup) and then I just have to change the index.txt
> instead of having
> 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2
> I put
> 1 1 1 1 1 1 1 1 1 1 1 1 7 7 7 7 7 7 7 7 7 7
Yes, that's the idea.
Also, from topup you have not only the field, you also have the relative positions of the different b=0 volumes in the <topupname>_movpars.txt file. And it can potentially be useful to use that information in eddy.
Let's say you have acquired both PE+ and PE- data like this
PE+ = { b0 dwi dwi dwi b0 dwi dwi dwi}
PE- = { b0 dwi dwi dwi b0 dwi dwi dwi}
and that you make a topup --imain file like
tp = { b0-PE+ b0-PE+ b0-PE- b0-PE- }
with a corresponding four entry acqparams.txt file and run topup.
You would then make a "total" data file for eddy like
ed = { b0-PE+ dwi-PE+ dwi-PE+ dwi-PE+ b0-PE+ dwi-PE+ dwi-PE+ dwi-PE+ b0-PE- dwi-PE- dwi-PE- dwi-PE- b0-PE- dwi-PE- dwi-PE- dwi-PE- }
and your index file would be
index.txt = { 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 }
where the entries in the acqparams.txt is the same for 1 and 2 and for 2 and 3 BUT where the movement parameters in the <topupnam>_movpars.txt file are different.
Admittedly it seems like eddy is capable of finding the correct movement parameters even without this "initialisation" from topup, but I didn't know that when I started designing eddy.
Jesper
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> thanks
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> Romain
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