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Dear Jesper,

I should add that we only encounter this problem for some subjects but not for others…

Thanks!!!


> Am 29.10.2015 um 18:36 schrieb Theodor Rüber <[log in to unmask]>:
> 
> Dear Jesper,
> 
> Thank you for your answer! As I do not have a CUDA-gpu, I used eddy_openmp. However I get the following error message.
> 
> How would you proceed?
> 
> Thanks a lot!
> 
> Best,
> 
> Theodor.
> 
> Starting eddy...
> Segmentation violation, Address not mapped, Offending address = 0x402ee54d0
> eddy_openmp ) [0x4e3db3] [_&#65533;
> eddy_openmp ) [0x5255ce] [&#65533;Q@
> eddy_openmp ) [0x525d20] [&#65533;Q@
> eddy_openmp ) [0x451022] [&#65533;Q@
> eddy_openmp ) [0x45279e] [&#65533;Q@
> eddy_openmp ) [0x4479ac] [&#65533;Q@
> eddy_openmp ) [0x458db6] [&#65533;Q@
> ./eddy_current_correction-1: Zeile 6 [i.e. line 6 (of the batch)]: 23639 Speicherzugriffsfehler [i.e. "segmentation fault"](Speicherabzug geschrieben) [i.e. memory snapshot written] eddy_openmp --imain=${sbj}_dir81_merged_LR_RL_gdc --mask=${sbj}_b0_topup_brain_mask --acqp=acqparms.txt --index=eddy_param.txt --bvecs=${sbj}_dir81_merged_LR_RL.bvec --bvals=${sbj}_dir81_merged_LR_RL.bval --topup=${sbj}_b0_topup_results --out=${sbj}_eddy_corr_data
> 
> 
> 
> Dear Theodore,
> 
>> Thank you for your answer:
>> "ls ${FSLDIR}/bin/eddy*" gives you
>> "eddy_combine eddy_correct eddy_cuda eddy_openmp”
> 
> the executables you want to use are eddy_cuda or eddy_openmp depending on if you have a CUDA-gpu box on your system or not. If you do, then I strongly recommend using eddy_cuda. If not you should use eddy_openmp.
> 
> The latter is multi-threaded and will potentially take as many threads as it can get its hands on, which may not be what you want. In that case you can use the environment variable OMP_NUM_THREADS and set it to a suitable value.
> 
> If you prefer to have an executable called eddy I suggest you make a link from ${FSLDIR}/bin/eddy to ${FSLDIR}/bin/eddy_* where * is the version you decide to use.
> 
> Jesper