Great it is now working perfectly.
Topup is excellent.
cheers
mich
On 1 Oct 2012, at 20:19, Stamatios Sotiropoulos wrote:
> Sorry that's probably a mistake in the help menu. You need --imain=DWI (instead of --in) and also --datain=acqparams.txt, where this is the text file you used in topup.
>
> Cheers
> Stam
>
>
>
> ----- Original Message ----- From: "Michel Thiebaut de Schotten" <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Monday, October 01, 2012 7:49 PM
> Subject: Re: [FSL] Topup application of generated "map"
>
>
> Dear experts,
>
> I tried topup but when using applytopup as follow
> applytopup -in=DWI --topup=my_output --inindex=1 --method=jac --interp=spline --out=hifi
>
>
> Here is what happen...
>
>
> Part of FSL (build 500)
> applytopup (Version 1.0)
> Copyright(c) 2009, University of Oxford (Jesper Andersson)
>
> Usage:
> applytopup -in=topdn,botup --topup=mytu --inindex=1,2 --out=hifi
> applytopup -in=topdn --topup=mytu --inindex=1 --method=jac --interp=spline --out=hifi
>
>
> Compulsory arguments (You MUST set one or more of):
> -i,--imain comma separated list of names of input image (to be corrected)
> -a,--datain name of text file with PE directions/times
> -x,--inindex comma separated list of indicies into --datain of the input image (to be corrected)
> -t,--topup name of field/movements (from topup)
> -o,--out basename for output (warped) image
>
> Optional arguments (You may optionally specify one or more of):
> -m,--method Use jacobian modulation (jac) or least-squares resampling (lsr), default=lsr.
> -n,--interp interpolation method {trilinear,spline}, default=spline
> -d,--datatype Force output data type [char short int float double].
> -v,--verbose switch on diagnostic messages
> -h,--help display this message
>
>
>
> -=: Option doesn't exist!
>
>
> I checked and everything should work but is doesn't.
> Any idea?
> Thanks,
> Kind regards,
>
> Michel
>
>
> On 1 Oct 2012, at 19:27, Ackerman, JosephJr. wrote:
>
>> thank you very much
>>
>> Joseph Ackerman Jr
>> Cell: 314-623-2605
>> ________________________________________
>> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Stamatios Sotiropoulos [[log in to unmask]]
>> Sent: Monday, October 01, 2012 1:26 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] Topup application of generated "map"
>>
>> Hi Joseph,
>>
>> You do not necessarily need to have the full dataset acquired with both phase encoding directions. Once you have run topup on a single pair (or multiple pairs) of b0s you can apply the results to your dataset.
>>
>> Run applytopup -h to get the help menu. You will see that there are two examples under Usage. The second is appropriate for your case (i.e. data with a single phase encoding direction). You just need to make sure that the --inindex points to an entry in acqparams.txt that refers to a b0 with the same phase-encoding direction as the data you are attempting to correct.
>>
>> Cheers
>> Stam
>>
>>
>>
>>
>> On 1 Oct 2012, at 19:16, Joseph Ackerman wrote:
>>
>>> I am new to Topup but have been successful at generating the "results_fieldcoef" and "results_movpar" files. The data set I am working with is a multi-volume diffusion (including b0) with positive phase-encode and a b0 with a negative phase-encoding. The hope / plan was to generate a field map type correction from topup using the two b0s since they have opposite phase encodes.
>>>
>>> Reading more of the topup and applytopup documentation it appears, and perhaps I am misunderstanding, that applytopup expects two "full" data sets, one positive and one negative, (in my case I only have one, positive) and it will use the output from topup to correct each pair of images. Is there anyway to use the output from topup without having a pair of diffusion data? Can the output be rationally used (or modified) to correct the distortions (from phase)?
>>>
>>> Thanks for any suggestions.
>>>
>>
>> ________________________________
>>
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