Thank you Jesper for your quick response
Indeed, i used the b02b0.cnf configuration file (it is included in FSL right ?, i don't need to download it ? because i just wrote the file name)
The output from topup looks pretty good, (i don't have much experience with field map but i don't see any problem)
the minimum value is -245.7 and the maximum is 289.7
i see no problem on the edge of the FOV
i can join the fout file if you want
Thanks again for your help
Christophe
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De : FSL - FMRIB's Software Library [[log in to unmask]] de la part de Jesper Andersson [[log in to unmask]]
Envoyé : mercredi 25 février 2015 11:23
À : [log in to unmask]
Objet : Re: [FSL] Problem with eddy
Dear Christophe,
i have seen something similar to this. That time it was because topup hadn’t converged properly, which was in turn caused by not using the recommended configuration file (b02b0.cnf). Can you please confirm that it was used, and also that the output from topup looks good. Look in particular for very large values at the edge of the FOV in the —fout output.
Jesper
On 25 Feb 2015, at 09:26, Christophe Maggia <[log in to unmask]> wrote:
> Hello everyone
>
> I'm trying to use eddy after topup to correct susceptibility and eddy current distorsions on DTI images (with 32 directions)
> topup is working very well but when i want to use eddy i get a weird error.
> At first, i thought it was a memory problem, but i tested it with another computer with the same results.
>
> my command line is :
> eddy --imain=MAP-VS-287_DTI_32_dir_SENSEmcverter.nii --mask=b0_Pbrain_mask.nii.gz --index=index.txt --acqp=acqparams.txt --bvecs=MAP-VS-287_DTI_32_dir.bvec --bvals=MAP-VS-287_DTI_32_dir.bval --fwhm=0 --topup=my_topup_results --flm=quadratic --out=DTI_ec.nii
>
> and i get this
>
> Running Register
> Segmentation violation, Address not mapped, Offending address = 0x512ae0000
> eddy 0x000000010010ad86 SPLINTERPOLATOR::Splinterpolator<float>::value_at(double const*) const
> eddy 0x00000001000c77d0 NEWIMAGE::volume<float>::splineinterpolate(float, float, float) const
> eddy 0x00000001000e5f20 NEWIMAGE::volume<float>::interpolate(float, float, float) const
> eddy 0x000000010002a084 void NEWIMAGE::raw_general_transform<float>(NEWIMAGE::volume<float> const&, NEWMAT::Matrix const&, NEWIMAGE::volume4D<float> const&, std::vector<int, std::allocator<int> > const&, std::vector<int, std::allocator<int> > const&, NEWMAT::Matrix const*, NEWMAT::Matrix const*, NEWIMAGE::volume<float>&, NEWIMAGE::volume4D<float>&, NEWIMAGE::volume<char>*)
> eddy 0x000000010002b3d4 void NEWIMAGE::affine_transform<float>(NEWIMAGE::volume<float> const&, NEWMAT::Matrix const&, NEWIMAGE::volume<float>&, NEWIMAGE::volume<char>&)
> eddy 0x0000000100019269 EDDY::ECScan::field_for_model_to_scan_transform(boost::shared_ptr<NEWIMAGE::volume<float> const>, NEWIMAGE::volume<float>*, NEWIMAGE::volume<float>*) const
> eddy 0x0000000100030f2c EDDY::EddyUtils::transform_model_to_scan_space(NEWIMAGE::volume<float> const&, EDDY::ECScan const&, boost::shared_ptr<NEWIMAGE::volume<float> const>, bool, NEWIMAGE::volume<float>&, NEWIMAGE::volume<float>*, NEWIMAGE::volume4D<float>*)
> eddy 0x0000000100036044 EDDY::EddyUtils::param_update(NEWIMAGE::volume<float> const&, boost::shared_ptr<NEWIMAGE::volume<float> const>, NEWIMAGE::volume<float> const&, EDDY::Parameters, bool, EDDY::ECScan&, NEWMAT::ColumnVector*)
> eddy 0x0000000100004cfc Register(EDDY::EddyCommandLineOptions const&, EDDY::ScanType, EDDY::ECScanManager&, unsigned int, NEWMAT::Matrix&, NEWMAT::Matrix&)
> eddy 0x0000000100005e7d main
> eddy 0x0000000100001ca8 start
> ??? 0x000000000000000b 0x0
>
>
> The "Offending address" is almost the same everytime 0x512******
> Do anyone know what i can do to make it work ? Please
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