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Hello,
 If you have a cuda-capable system, then you can use the cuda version of eddy ( cuda_eddy ) otherwise you can use the openMP version ( eddy_openmp ) which will try to use all the cpu cores in your system. Note that running eddy may take some time..

Kind Regards
Matthew
On 11 Aug 2016, at 08:51, Julien Besle <[log in to unmask]> wrote:

Thanks for your message Enes,

There is nt eddy command under /usr/lib/fsl/5.0/. In fact there is no fsl directory in /usr/lib

When I try to find any file named eddy* on my system, this is what I find:

> find / -name "eddy*"
/usr/local/fsl_5.0/bin/eddy_combine
/usr/local/fsl_5.0/bin/eddy_correct
/usr/local/fsl_5.0/bin/eddy_cuda
/usr/local/fsl_5.0/bin/eddy_openmp
/usr/local/fsl_5.0/src/fdt/eddy_combine.cc
/usr/local/fsl_5.0/src/fdt/eddy_correct
/usr/local/fsl_5.0/doc/wiki/attachments/eddy(2f)Faq
/usr/local/fsl_5.0/doc/wiki/attachments/eddy
/usr/local/fsl_5.0/doc/wiki/attachments/eddy(2f)UsersGuide
/usr/local/fsl_5.0/doc/wiki/eddy.html
/usr/local/fsl_5.0/doc/wiki/eddy(2f)Faq.html
/usr/local/fsl_5.0/doc/wiki/eddy(2f)UsersGuide.html
/usr/local/fsl_5.0/doc/wiki/eddy(2f)Contents.html
/usr/local/fsl_5.0/doc/eddy
/usr/local/fsl_5.0/refdoc/eddy
/usr/local/bin/eddy_correct
/usr/local/fsl_4.1.6/bin/eddy_correct
/usr/local/fsl_4.1.6/src/fdt/doc/fdt_images/eddy.tif
/usr/local/fsl_4.1.6/src/fdt/doc/fdt_images/eddy2.gif
/usr/local/fsl_4.1.6/src/fdt/doc/fdt_images/eddy.gif
/usr/local/fsl_4.1.6/src/fdt/eddy_correct
/usr/local/fsl_4.1.6/doc/fdt/fdt_images/eddy.tif
/usr/local/fsl_4.1.6/doc/fdt/fdt_images/eddy2.gif
/usr/local/fsl_4.1.6/doc/fdt/fdt_images/eddy.gif

+ a lot of non-searchable locations

My linux system is a fairly old version and was not supported by FSL installer (even thought it did install). Could it be that eddy didn't get compiled?

Thanks

Julien

On 11/08/2016 07:11, Enes Albay - انس الباى wrote:
[log in to unmask]" type="cite" class="">
Hi Julien,

I am not sure but I think your acqparams.txt file must contain three lines because you merge three images:
Your acqparams.txt must be like this:

0 -1 0 1
0 1 0 1
0 -1 0 1

Also yout eddy command must be under /usr/lib/fsl/5.0 directory. If you see eddy under this directory but you can not call it, you must add this path to your PATH environment variable. 

To add this path your PATH environment variable please add the following lines to the end of your ~/.bashrc file

PATH=$PATH:/usr/lib/fsl/5.0
export PATH








On Thu, Aug 11, 2016 at 8:30 AM, Julien Besle <[log in to unmask]> wrote:
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]UK> 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




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--
Enes Albay


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Julien Besle
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