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Thank you again Jesper I uploaded it (fieldmapCMaggia.nii) I calculated the readout time with the recommendations of Philips, so it should be fine I don't know if you have seen my previous message but i tried to use the output file with applytopup and i also have an error : ApplyTopup : : msg=Invalid combination of phase-encode vectors for least-square restoration maybe the two are linked but i still can't find a solution... Christophe ________________________________ De : FSL - FMRIB's Software Library [[log in to unmask]] de la part de Jesper Andersson [[log in to unmask]] Envoyé : jeudi 26 février 2015 11:46 À : [log in to unmask] Objet : Re: [FSL] Problem with eddy Dear Christophe, 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) that should be sufficient. 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 these are quite high and might be indicative of an error. Though if you just guessed the readout time they might still be kosher. i see no problem on the edge of the FOV i can join the fout file if you want Yes, can you please upload it to https://oxfile.ox.ac.uk/oxfile/work/extBox?id=72139C7E463068D5F Jesper Thanks again for your help Christophe ________________________________________ De : FSL - FMRIB's Software Library [[log in to unmask]<mailto:[log in to unmask]>] de la part de Jesper Andersson [[log in to unmask]<mailto:[log in to unmask]>] Envoyé : mercredi 25 février 2015 11:23 À : [log in to unmask]<mailto:[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]<mailto:[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