Dear Romain,
>
> ok but then I get the error
>
> Terminate called after throwing an instance of ‘NEWMAT::IndexException’
>
> this is the same as Stefano Marenco (23/10/2012) so I have to wait for the update... (?)
Yes, I am afraid so. In the general rush before the FSL 5 release I managed to introduce that bug immediately before the release :(
>
> I test both (with the same error) :
> 1_ compute topup only on B0 or
> 2_ compute topup on the all
>
> I just see in an other post that you advise the first one. but then how do you handel the index and acqp.txt parameters : in the eddy comand you specify the acqp and index for the full 4D data set (blip_up and blip_down concatenate) whereas topup was run only on the B0. (or in my case on several B0 since I have one B0 each 10 directions).
> how do you specify the relation between the different B0 input of topup and the all data set input of eddy ?
If you have two b0 scans that you have run topup on you will have one field and two different ways of applying it (corresponding to the two different b0 acquisitions). You then need to make sure that each dwi has the field applied in the correct way. Let us say the b0 input file you ran topup on was
b0 = { PE+ , PE- }
and that you have an input file for eddy that looks like
data = { PE-, PE-, PE-, PE+, PE+, PE+ }
your index file should then be
index.txt = { 2 2 2 1 1 1 }
implying the the three first volumes should be corrected in accordance with the second scan in b0 and the the last three should be corrected in accordance with the first volume in b0.
I know it is kind of messy, but I really couldn't come up with an easier way to provide eddy with the information.
Jesper
>
>
> thanks for your help
>
> Romain
>
>
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