Hi there,
topup is now openly supported. If you go to what's new in FSL 5 you'll find links to the documentation (maybe that's what you did?).
Jesper
On 26 Sep 2012, at 16:01, Marenco, Stefano (NIH/NIMH) [E] wrote:
> Is topup now part of the official distribution? I could not find it among the main list of tools, although when I search for topup I can find a Users guide and an example. Is this now openly supported or still in testing?
>
> Stefano Marenco, MD
> NIMH/CBDB
> 10 Center Drive, Bldg 10 room 3C103
> Bethesda MD 20892
> Tel 301 435-8964
> Fax 301 480-7795
> Email: [log in to unmask]
>
>
> -----Original Message-----
> From: Jesper Andersson [mailto:[log in to unmask]]
> Sent: Wednesday, September 26, 2012 3:58 AM
> To: [log in to unmask]
> Subject: Re: [FSL] TopUp --datain
>
> 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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