Hi Jesper,
thanks for the reply. The reason to try the non-standard settings such
as --fwhm was that we were testing some settings in the sequence which
has increased eddy current artefacts. However, we have realised that
the distortions were not uniform throughout the acquisition which was
most likely the cause of our problems. I guess even setting FWHM to
non-zero value won't eventually fix that :(
Cheers
Pavel
On 21 April 2016 at 12:51, Jesper Andersson
<[log in to unmask]> wrote:
> Dear Pavel,
>
> yes, I am afraid this is an eddy bug in the non-GPU version. It has been
> corrected for the next version.
>
> Did you have a lot of subject movement in the data for which fwhm=0 was
> unsatisfactory? If not, I would be interested in taking at look at them if
> that is ok with you? If so, can you please upload an example data set in a
> tar-ball with all the files alluded to on the command line to
> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=72139C7E463068D5F
> and also send me the full eddy command that gave unsatisfactory results?
>
> Jesper
>
>
>
> On 19 Apr 2016, at 10:52, Pavel Hok <[log in to unmask]> wrote:
>
> Dear FSL experts,
>
> although I have noticed similar posts I guess this is a separate
> problem. Until now, eddy (eddy_openmp) was running fine for me.
> However, I was quite unsatisfied with the eddy current correction
> results of my last analysis so I tried the --fwhm=10,0,0,0,0 option as
> suggested on the website. Unfortunately, eddy crashes immediately with
> the following error whenever I try the command. Without the option it
> works again so I guess it cannot be problem with the b vectors.
>
> eddy_openmp --imain=/mydir/nifti/dti.nii.gz
> --mask=/mydir/topup/nodif_brain_mask.nii.gz
> --acqp=/mydir/topup/topup.txt --index=/mydir/topup/index.txt
> --topup=/mydir/topup/topup --out=/mydir/eddy/data
> --bvecs=/mydir/topup/bvecs --bvals=/mydir/topup/bvals
> --fwhm=10,0,0,0,0
> Segmentation violation, Invalid permission for address, Offending
> address = 0x7f8177f49000
> /myscriptdir/fdt_pipe.sh: line 340: 19559 Segmentation fault $1
>
> Any ideas? Thanks in advance!
>
> Cheers
>
> Pavel
>
> --
> -------------------------------------------------------------------------------
> -- MUDr. Pavel Hok
> -------------------------------------------------------------------------------
> -- Laboratoř funkční magnetické rezonance
> -- Neurologická klinika
> -- Lékařská fakulta
> -- Univerzita Palackého v Olomouci
> -- Fakultní nemocnice Olomouc
> -------------------------------------------------------------------------------
> -- Laboratory of functional magnetic resonance imaging
> -- Department of Neurology
> -- Faculty of Medicine and Dentistry
> -- Palacky University Olomouc
> -- University Hospital Olomouc
> -- Czech Republic
> -------------------------------------------------------------------------------
> -- I.P. Pavlova 6, 775 20 Olomouc
> -- web: fmri.upol.cz
> -- tel.: +420 588 443 418
> -- e-mail: [log in to unmask]
> -------------------------------------------------------------------------------
>
>
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