Hello!
I tried to run the pipeline that I used for the study on the participant of a colleague who used exactly the same sequence. When I try to run the Eddy current correction with this command:
dwifslpreproc DWI_deno7_unr.mif DWI_deno7_unr_epi_eddy.mif -rpe_header -se_epi b0_pair.mif -topup_options " --scale=1" -eddy_options " --repol --ol_type=both --niter=8 --fwhm=10,8,4,2,0,0,0,0 --data_is_shelled --cnr_maps --residuals --mporder=7 --s2v_niter=5 --s2v_lambda=5 --s2v_interp=trilinear --slm=linear" -eddy_slspec=/media/u0136350/EleD/DWI/myslspec_mb2.txt -nocleanup
I get an error regarding the unknown slice encoding direction:
dwifslpreproc: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwifslpreproc:
dwifslpreproc: Generated scratch directory: /media/u0136350/EleD/DWI/A24/dwifslpreproc-tmp-ZKY7AV/
Command: mrconvert /media/u0136350/EleD/DWI/A24/DWI_deno7_unr.mif /media/u0136350/EleD/DWI/A24/dwifslpreproc-tmp-ZKY7AV/dwi.mif -json_export /media/u0136350/EleD/DWI/A24/dwifslpreproc-tmp-ZKY7AV/dwi.json
Command: mrconvert /media/u0136350/EleD/DWI/A24/b0_pair.mif /media/u0136350/EleD/DWI/A24/dwifslpreproc-tmp-ZKY7AV/se_epi.mif
dwifslpreproc: Changing to scratch directory (/media/u0136350/EleD/DWI/A24/dwifslpreproc-tmp-ZKY7AV/)
dwifslpreproc: No slice encoding direction information present; assuming third axis corresponds to slices
Command: mrinfo dwi.mif -export_grad_mrtrix grad.b
Command: mrconvert se_epi.mif topup_in.nii -strides -1,+2,+3,+4 -export_pe_table topup_datain.txt
Command: topup --imain=topup_in.nii --datain=topup_datain.txt --out=field --fout=field_map.nii.gz --config=/usr/local/fsl/etc/flirtsch/b02b0.cnf --verbose --scale=1
Command: mrinfo dwi.mif -export_pe_eddy applytopup_config.txt applytopup_indices.txt
Command: dwiextract dwi.mif -pe 0.0,-1.0,0.0,0.0173 - | mrconvert - dwi_pe_1.nii -strides -1,+2,+3,+4 -json_export dwi_pe_1.json
Command: applytopup --imain=dwi_pe_1.nii --datain=applytopup_config.txt --inindex=1 --topup=field --out=dwi_pe_1_applytopup.nii --method=jac
Command: mrconvert dwi_pe_1_applytopup.nii.gz dwi_pe_1_applytopup.mif -json_import dwi_pe_1.json
Command: dwi2mask dwi_pe_1_applytopup.mif - | maskfilter - dilate - | mrconvert - eddy_mask.nii -datatype float32 -strides -1,+2,+3
Command: mrconvert dwi.mif eddy_in.nii -strides -1,+2,+3,+4 -export_grad_fsl bvecs bvals -export_pe_eddy eddy_config.txt eddy_indices.txt
Command: eddy_cuda10.2 --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --repol --ol_type=both --niter=8 --fwhm=10,8,4,2,0,0,0,0 --data_is_shelled --cnr_maps --residuals --mporder=7 --s2v_niter=5 --s2v_lambda=5 --s2v_interp=trilinear --slm=linear --slspec=slspec.txt --out=dwi_post_eddy --verbose
dwifslpreproc: CUDA version of ‘eddy’ was not successful; attempting OpenMP version
Command: eddy_openmp --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --repol --ol_type=both --niter=8 --fwhm=10,8,4,2,0,0,0,0 --data_is_shelled --cnr_maps --residuals --mporder=7 --s2v_niter=5 --s2v_lambda=5 --s2v_interp=trilinear --slm=linear --slspec=slspec.txt --out=dwi_post_eddy --verbose
dwifslpreproc: [ERROR] eddy* --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --repol --ol_type=both --niter=8 --fwhm=10,8,4,2,0,0,0,0 --data_is_shelled --cnr_maps --residuals --mporder=7 --s2v_niter=5 --s2v_lambda=5 --s2v_interp=trilinear --slm=linear --slspec=slspec.txt --out=dwi_post_eddy --verbose (app.py:197)
dwifslpreproc: [ERROR] Information from failed command:
dwifslpreproc:
=============
eddy_cuda10.2
=============
===========
eddy_openmp
===========
Reading images
Performing volume-to-volume registration
Running Register
Loading prediction maker
Evaluating prediction maker model
Calculating parameter updates
Iter: 0, Total mss = 10.631
Loading prediction maker
Evaluating prediction maker model
Calculating parameter updates
Iter: 1, Total mss = 7.357
Loading prediction maker
Evaluating prediction maker model
Calculating parameter updates
Iter: 2, Total mss = 11.6926
Loading prediction maker
Evaluating prediction maker model
Calculating parameter updates
Iter: 3, Total mss = 25.4209
Loading prediction maker
Evaluating prediction maker model
Calculating parameter updates
Iter: 4, Total mss = 26.8524
Loading prediction maker
Evaluating prediction maker model
Calculating parameter updates
Iter: 5, Total mss = 26.8271
Loading prediction maker
Evaluating prediction maker model
Calculating parameter updates
Iter: 6, Total mss = 26.825
Loading prediction maker
Evaluating prediction maker model
Calculating parameter updates
Iter: 7, Total mss = 26.825
Setting scan 51 as b0 shape-reference.
Running sm.ApplyB0LocationReference
Running sm.PolateB0MovPar
Running Register
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: -3.042537
0.325092
8.655804
0.527045
-1.529125
-2.803158
Calculating parameter updates
Iter: 0, Total mss = 0.316909
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: -0.152427
0.322832
8.441536
3.444422
1.511387
0.067826
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: -0.013886
0.321636
8.891357
3.294751
1.555792
0.099647
Calculating parameter updates
Iter: 1, Total mss = 0.322864
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 0.802981
0.330027
8.572978
4.040027
2.359443
1.245252
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 1.610027
0.320510
8.657087
4.832754
3.117784
1.996416
Calculating parameter updates
Iter: 2, Total mss = 0.552125
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 0.771755
0.335199
8.281189
4.149102
2.494768
1.635291
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 0.149053
0.340291
8.624656
3.386605
1.908300
1.061929
Calculating parameter updates
Iter: 3, Total mss = 1.357532
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 0.627743
0.342004
7.891729
3.846422
2.303498
1.548995
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 0.015467
0.331952
8.483831
3.463324
1.699053
0.878903
Calculating parameter updates
Iter: 4, Total mss = 1.355804
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 0.562790
0.338471
8.126419
3.788968
2.303188
1.492092
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 1.060894
0.350497
9.950103
4.349244
2.817090
2.038128
Calculating parameter updates
Iter: 5, Total mss = 1.376474
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 0.557074
0.341915
8.122693
3.828745
2.272494
1.457832
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 0.977831
0.341157
8.242885
4.326150
2.775069
1.927374
Calculating parameter updates
Iter: 6, Total mss = 1.371848
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: 0.452134
0.349856
7.712988
3.848296
2.230242
1.487293
Loading prediction maker
Evaluating prediction maker model
Estimated hyperparameters: -0.494201
0.338000
8.152722
2.819806
1.281971
0.442445
Calculating parameter updates
Iter: 7, Total mss = 1.361307
Setting scan 47 as shell shape-reference for shell 0 with b-value= 700.000000
Setting scan 56 as shell shape-reference for shell 1 with b-value= 1200.000000
Setting scan 48 as shell shape-reference for shell 2 with b-value= 2800.000000
Running sm.ApplyDWILocationReference
Checking shell alignment along PE-direction (running PostEddyAlignShellsAlongPE)
Aligning shells (running PostEddyAlignShells)
Performing slice-to-volume registration
Setting slice-to-volume order to 7
Running Register
Loading prediction makerMat::operator(): index out of bounds
Mat::operator(): index out of bounds
Mat::operator(): index out of boundsMat::operator(): index out of bounds
Mat::operator(): index out of bounds
EDDY::: ECScanClasses.cpp::: void EDDY::ECScan::get_slice_stack_and_zcoords(const NEWIMAGE::volume<float>&, std::shared_ptr<const NEWIMAGE::volume<float> >, NEWIMAGE::volume<float>&, NEWIMAGE::volume<float>&, NEWIMAGE::volume<float>&, bool) const: Exception thrown
EDDY::: ECScanClasses.cpp::: void EDDY::ECScan::get_slice_stack_and_zcoords(const NEWIMAGE::volume<float>&, std::shared_ptr<const NEWIMAGE::volume<float> >, NEWIMAGE::volume<float>&, NEWIMAGE::volume<float>&, NEWIMAGE::volume<float>&, bool) const: Exception thrown
EDDY::: ECScanClasses.cpp::: NEWIMAGE::volume<float> EDDY::ECScan::transform_slice_to_vol_to_model_space(const NEWIMAGE::volume<float>&, std::shared_ptr<const NEWIMAGE::volume<float> >, const NEWIMAGE::volume<float>*, NEWIMAGE::volume<float>&, bool) const: Exception thrown
EDDY::: ECScanClasses.cpp::: NEWIMAGE::volume<float> EDDY::ECScan::transform_slice_to_vol_to_model_space(const NEWIMAGE::volume<float>&, std::shared_ptr<const NEWIMAGE::volume<float> >, const NEWIMAGE::volume<float>*, NEWIMAGE::volume<float>&, bool) const: Exception thrown
EDDY::: ECScanClasses.cpp::: NEWIMAGE::volume<float> EDDY::ECScan::GetUnwarpedIma(std::shared_ptr<const NEWIMAGE::volume<float> >, NEWIMAGE::volume<float>&) const: Exception thrown
EDDY::: ECScanClasses.cpp::: NEWIMAGE::volume<float> EDDY::ECScan::GetUnwarpedIma(std::shared_ptr<const NEWIMAGE::volume<float> >, NEWIMAGE::volume<float>&) const: Exception thrown
EDDY::: ECScanClasses.cpp::: void EDDY::ECScan::get_slice_stack_and_zcoords(const NEWIMAGE::volume<float>&, std::shared_ptr<const NEWIMAGE::volume<float> >, NEWIMAGE::volume<float>&, NEWIMAGE::volume<float>&, NEWIMAGE::volume<float>&, bool) const: Exception thrown
EDDY::: ECScanClasses.cpp::: void EDDY::ECScan::get_slice_stack_and_zcoords(const NEWIMAGE::volume<float>&, std::shared_ptr<const NEWIMAGE::volume<float> >, NEWIMAGE::volume<float>&, NEWIMAGE::volume<float>&, NEWIMAGE::volume<float>&, bool) const: Exception thrown
Mat::operator(): index out of boundsEDDY::: ECScanClasses.cpp::: NEWIMAGE::volume<float> EDDY::ECScan::transform_slice_to_vol_to_model_space(const NEWIMAGE::volume<float>&, std::shared_ptr<const NEWIMAGE::volume<float> >, const NEWIMAGE::volume<float>*, NEWIMAGE::volume<float>&, bool) const: Exception thrown
=============
eddy_cuda10.2
=============
eddy_cuda10.2: error while loading shared libraries: libcublas.so.10: cannot open shared object file: No such file or directory
===========
eddy_openmp
===========
terminate called recursively
terminate called after throwing an instance of '
dwifslpreproc:
dwifslpreproc: [ERROR] For debugging, inspect contents of scratch directory: /media/u0136350/EleD/DWI/A24/dwifslpreproc-tmp-ZKY7AV/
[ERROR] For debugging, inspect contents of scratch directory: /media/u0136350/EleD/DWI/A24/dwifslpreproc-tmp-ZRDHE9/
()
Why could this be and how could I solve it?
Thank you very much in advance,
Geraldine.