Eddy_openmp error

Hi everyone! I got an error when using dwifslpreproc! I used the code "dwifslpreproc denoised.mif proc.mif -fslgrad dwi.bvec dwi.bval -rpe_none -pe_dir AP -eddy_options “–data_is_shelled --slm=linear” ". But I got --data_is_shelled: Option doesn’t exist. I’ve tried adding Spaces or = before --, but it doesn’t work

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Hi @Qianhui_Xu,

Can you provide the full output of the command when running with the -debug option? You can copy/paste the output into your post, just make sure to enclose it in triple backticks (```) to preserve the formatting as it was – it really helps to have the exact output, not the user’s interpretation of it, since that allows us to figure which exact line of code the error originates from, etc.

All the best,

Dear Donald, thank you very much for your prompt reply! Below is the complete information of the output error.txt. I hople it helps.

(mrtrix) mri@mri:~/dti_network_hc/DTI_NET/sub001/DTI1$ dwifslpreproc dwi_denoise_gib.mif dwi_preproc.mif -fslgrad DWI.bvec DWI.bval -rpe_none -pe_dir AP -eddy_options " --data_is_shelled --slm=linear" -force
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: Generated scratch directory: /home/mri/dti_network_hc/DTI_NET/sub001/DTI1/dwifslpreproc-tmp-6M4BJD/
Command:  mrconvert /home/mri/dti_network_hc/DTI_NET/sub001/DTI1/dwi_denoise_gib.mif /home/mri/dti_network_hc/DTI_NET/sub001/DTI1/dwifslpreproc-tmp-6M4BJD/dwi.mif -fslgrad /home/mri/dti_network_hc/DTI_NET/sub001/DTI1/DWI.bvec /home/mri/dti_network_hc/DTI_NET/sub001/DTI1/DWI.bval -json_export /home/mri/dti_network_hc/DTI_NET/sub001/DTI1/dwifslpreproc-tmp-6M4BJD/dwi.json
dwifslpreproc: Changing to scratch directory (/home/mri/dti_network_hc/DTI_NET/sub001/DTI1/dwifslpreproc-tmp-6M4BJD/)
dwifslpreproc: Total readout time not provided at command-line; assuming sane default of 0.1
Command:  mrinfo dwi.mif -export_grad_mrtrix grad.b
Command:  dwi2mask dwi.mif - | maskfilter - dilate - | mrconvert - eddy_mask.nii -datatype float32 -strides -1,+2,+3
Command:  mrconvert dwi.mif -import_pe_table dwi_manual_pe_scheme.txt eddy_in.nii -strides -1,+2,+3,+4 -export_grad_fsl bvecs bvals -export_pe_eddy eddy_config.txt eddy_indices.txt
Command:  eddy_cuda --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --data_is_shelled --slm=linear --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 --data_is_shelled --slm=linear --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 --data_is_shelled --slm=linear --out=dwi_post_eddy --verbose (app.py:196)
dwifslpreproc: [ERROR] Information from failed command:
               eddy_cuda: error while loading shared libraries: libcudart.so.6.0: cannot open shared object file: No such file or directory
               Part of FSL (build 509)
               Copyright(c) 2015, University of Oxford (Jesper Andersson)
               eddy --monsoon
               Compulsory arguments (You MUST set one or more of):
               	--imain	File containing all the images to estimate distortions for
               	--mask	Mask to indicate brain
               	--index	File containing indices for all volumes in --imain into --acqp and --topup
               	--acqp	File containing acquisition parameters
               	--bvecs	File containing the b-vectors for all volumes in --imain
               	--bvals	File containing the b-values for all volumes in --imain
               	--out	Basename for output
               Optional arguments (You may optionally specify one or more of):
               	--topup	Base name for output files from topup
               	--flm	First level EC model (linear/quadratic/cubic, default quadratic)
               	--slm	Second level EC model (none/linear/quadratic, default none)
               	--fwhm	FWHM for conditioning filter when estimating the parameters (default 0)
               	--niter	Number of iterations (default 5)
               	--fep	Fill empty planes in x- or y-directions
               	--interp	Interpolation model for estimation step (spline/trilinear, default spline)
               	--resamp	Final resampling method (jac/lsr, default jac)
               	--nvoxhp	# of voxels used to estimate the hyperparameters (default 1000)
               	--ff	Fudge factor for hyperparameter error variance (default 10.0)
               	--dont_sep_offs_move	Do NOT attempt to separate field offset from subject movement (default false)
               	--dont_peas	Do NOT perform a post-eddy alignment of shells (default false)
               	-v,--verbose	switch on diagnostic messages
               	-h,--help	display this message
               --data_is_shelled: Option doesn't exist!

Dear Qianhui,

The usage of -eddy_options is to add one space before --data_is_shelled. However, based on the eddy_openmp output, you are using an outdated FSL version; there are no “–data_is_shelled” or “–mporder” or other recent tools implemented in EDDY in the options. Ask your admin to update the FSL and I think then you’ll be good to go.