Hi Jesper
OK perfect this is what I collected (opposing phase encode + fieldmap).
Does it also mean that other dataset have to be processed with standard Eddy Current Distortion and not TopUp?
Thanks,
michel
On 26 Sep 2012, at 08:57, Jesper Andersson wrote:
> Hi Michel,
>
> as a little addendum to Saads reply I should stress that topup can only be used if the data was acquired in a way that allows it. I.e. if data was for example acquired twice with opposing phase-encode blips. Data that was acquired without planning to use topup is unlikely to be possible to process with topup.
>
> This is equivalent to other types of distortion correction where if for example one has not acquired fieldmaps one cannot use fieldmap based corrections.
>
> Good luck Jesper
>
>
> On 26 Sep 2012, at 09:49, Michel Thiebaut de Schotten wrote:
>
>> Dear experts,
>>
>> This morning I tried to run topup for the first time, to correct distortion on a DWI dataset.
>> Following the help menu I wrote the following command
>>
>> topup --imain=DWI.nii --datain=bvecs
>>
>> But the following error occurred:
>> TopupFileIO:: msg=TopupDatafileReader:: error reading file bvecs
>> What is supposed to be the --datain if not the Bvec?
>>
>> Thanks for your help an the new release of FSL,
>> Kind regards,
>>
>> Michel
>>
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