Hi Jesper
I tried adding --method==jac, but in this case, it returns immediately with no output (and no error)
I tried typing eddy, but there is no such command. Is it in a more recent version or is the binary located somewhere else? (I'm using FSL 5.0)
Thanks a lot
Julien
> On 10 Aug 2016, at 18:33, "Jesper Andersson" <[log in to unmask]> wrote:
>
> Dear Julien,
>
>>
>> I'm having problems running the applytopup command.
>>
>> We collected one DWI scan with 20 directions (b0 + 19*b=1000) as well as 2 smaller DWI scans with 3 b0 images of opposite phase encoding directions. I have run the following topup comand:
>>> topup --imain=15_16_17_PA_AP_AP --datain acqparams.txt --out=topup_params --iout=15_16_17_PA_AP_AP_corrected
>>
>> with
>>> more acqparams.txt:
>> 0 -1 0 1
>> 0 -1 0 1
>> 0 -1 0 1
>> 0 1 0 1
>> 0 1 0 1
>> 0 1 0 1
>> 0 1 0 1
>> and 15_16_17_PA_AP_AP.nii obtained using
>>> fslmerge -t 15_16_17_PA_AP_AP 15_PA 16_AP 17_AP
>> and 17_AP obtained using
>>> fslroi 17_AP 17-ep2d_advdiff_2mm 0 110 0 110 0 42 0 1
>>
>> I then want to apply the calculated fields with applytopup, but I get an error:
>>> applytopup --imain=17-ep2d_advdiff_2mm --datain=acqparams.txt --inindex=7 --topup=topup_params --out=17-ap2d_advdiff_2mm_corrected
>>
>> ApplyTopup:: msg=Invalid combination of phase-encode vectors for least-squares restoration
>> terminate called after throwing an instance of 'TOPUP::ApplyTopupException'
>> what(): ApplyTopup:: msg=Invalid combination of phase-encode vectors for least-squares restoration
>> Abort (core dumped)
>
> It is because the default resampling method is “least squares”, which you can only use if all dwis have been acquired twice with opposing PE directions. If you add --method=jac to your call I think you should be fine.
>
> Also, we no longer recommend using applytopup. We now recommend feeding the topup results into eddy, which will do essentially the same thing as applytopup, but in addition also correcting your dwis for eddy currents and subject movement.
>
> Jesper
This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it.
Please do not use, copy or disclose the information contained in this
message or in any attachment. Any views or opinions expressed by the
author of this email do not necessarily reflect the views of the
University of Nottingham.
This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system, you are advised to perform your own checks. Email
communications with the University of Nottingham may be monitored as
permitted by UK legislation.
|