(base) sajidhussain@sajidhussain-HP-EliteBook-840-G4:~/Desktop/mydataset$ dwifslpreproc ankit_den.mif ankit_den.preproc.mif -nocleanup -pe_dir AP -rpe_pair -se_epi b0_pair.mif -eddy_options " -slm=linear --data_is_shelled"

Hi everyone
I m new to this community. I have a question regarding distortion correction which is as follows:
While executing the following command:

(base) sajidhussain@sajidhussain-HP-EliteBook-840-G4:~/Desktop/mydataset$ dwifslpreproc ankit_den.mif ankit_den.preproc.mif -nocleanup -pe_dir AP -rpe_pair -se_epi b0_pair.mif -eddy_options "  -slm=linear --data_is_shelled"

all i got is as follows:

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/sajidhussain/Desktop/mydataset/dwifslpreproc-tmp-HXE56S/
Command:  mrconvert /home/sajidhussain/Desktop/mydataset/ankit_den.mif /home/sajidhussain/Desktop/mydataset/dwifslpreproc-tmp-HXE56S/dwi.mif -json_export /home/sajidhussain/Desktop/mydataset/dwifslpreproc-tmp-HXE56S/dwi.json
Command:  mrconvert /home/sajidhussain/Desktop/mydataset/b0_pair.mif /home/sajidhussain/Desktop/mydataset/dwifslpreproc-tmp-HXE56S/se_epi.mif
dwifslpreproc: Changing to scratch directory (/home/sajidhussain/Desktop/mydataset/dwifslpreproc-tmp-HXE56S/)
Command:  dirstat dwi.mif -output asym
dwifslpreproc: [WARNING] sampling of b=1000 shell is moderately asymmetric; distortion correction may benefit from use of: -eddy_options " ... --slm=linear ... "
dwifslpreproc: Total readout time not provided at command-line; assuming sane default of 0.1
Command:  mrinfo dwi.mif -export_grad_mrtrix grad.b
dwifslpreproc: 1 spatial axis of DWIs has non-even size; this will be automatically padded for compatibility with topup, and the extra slice erased afterwards
Command:  mrconvert se_epi.mif -coord 2 28 - | mrcat se_epi.mif - se_epi_pad2.mif -axis 2
Command:  mrconvert dwi.mif -coord 2 28 - | mrcat dwi.mif - dwi_pad2.mif -axis 2
Command:  mrconvert se_epi_pad2.mif topup_in.nii -import_pe_table se_epi_manual_pe_scheme.txt -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.img --config=/usr/local/fsl/etc/flirtsch/b02b0.cnf --verbose
Command:  mrconvert dwi_pad2.mif -import_pe_table dwi_manual_pe_scheme.txt - | mrinfo - -export_pe_eddy applytopup_config.txt applytopup_indices.txt
Command:  dwiextract dwi_pad2.mif -import_pe_table dwi_manual_pe_scheme.txt -pe 0.0,-1.0,0.0,0.1 - | mrconvert - dwi_pad2_pe_1.nii -strides -1,+2,+3,+4 -json_export dwi_pad2_pe_1.json
Command:  applytopup --imain=dwi_pad2_pe_1.nii --datain=applytopup_config.txt --inindex=1 --topup=field --out=dwi_pad2_pe_1_applytopup.nii --method=jac
Command:  mrconvert dwi_pad2_pe_1_applytopup.img dwi_pad2_pe_1_applytopup.mif -json_import dwi_pad2_pe_1.json
Command:  dwi2mask dwi_pad2_pe_1_applytopup.mif - | maskfilter - dilate - | mrconvert - eddy_mask.nii -datatype float32 -strides -1,+2,+3
Command:  mrconvert dwi_pad2.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_cuda9.1 --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field -slm=linear --data_is_shelled --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 -slm=linear --data_is_shelled --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 -slm=linear --data_is_shelled --out=dwi_post_eddy --verbose (app.py:197)
dwifslpreproc: [ERROR] Information from failed command:
               eddy_cuda9.1: error while loading shared libraries: libcublas.so.9.1: cannot open shared object file: No such file or directory
               Part of FSL (ID: 6.0.4:ddd0a010)
               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):
               	--mb	Multi-band factor
               	--mb_offs	Multi-band offset (-1 if bottom slice removed, 1 if top slice removed)
               	--slspec	Name of text file completely specifying slice/group acuistion. N.B. --slspec and --json are mutually exclusive.
               	--json	Name of .json text file with information about slice timing. N.B. --json and --slspec are mutually exclusive.
               	--mporder	Order of slice-to-vol movement model (default 0, i.e. vol-to-vol
               	--s2v_lambda	Regularisation weight for slice-to-vol movement. (default 1, reasonable range 1--10
               	--topup	Base name for output files from topup
               	--field	Name of file with susceptibility field (in Hz)
               	--field_mat	Name of rigid body transform for susceptibility field
               	--flm	First level EC model (movement/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)
               	--s2v_niter	Number of iterations for slice-to-vol (default 5)
               	--cnr_maps	Write shell-wise cnr-maps (default false)
               	--residuals	Write residuals (between GP and observations), (default false)
               	--fep	Fill empty planes in x- or y-directions (default false)
               	--interp	Interpolation model for estimation step (spline/trilinear, default spline)
               	--s2v_interp	Slice-to-vol interpolation model for estimation step (spline/trilinear, default trilinear)
               	--resamp	Final resampling method (jac/lsr, default jac)
               	--nvoxhp	# of voxels used to estimate the hyperparameters (default 1000)
               	--initrand	Seeds rand for when selecting voxels (default 0=no seeding)
               	--ff	Fudge factor for hyperparameter error variance (default 10.0)
               	--repol	Detect and replace outlier slices (default false))
               	--ol_nstd	Number of std off to qualify as outlier (default 4)
               	--ol_nvox	Min # of voxels in a slice for inclusion in outlier detection (default 250)
               	--ol_type	Type of outliers, slicewise (sw), groupwise (gw) or both (both). (default sw)
               	--ol_pos	Consider both positive and negative outliers if set (default false)
               	--ol_sqr	Consider outliers among sums-of-squared differences if set (default false)
               	--estimate_move_by_susceptibility	Estimate how susceptibility field changes with subject movement (default false)
               	--mbs_niter	Number of iterations for MBS estimation (default 10)
               	--mbs_lambda	Weighting of regularisation for MBS estimation (default 10)
               	--mbs_ksp	Knot-spacing for MBS field estimation (default 10mm)
               	--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)
               	--data_is_shelled	Assume, don't check, that data is shelled (default false)
               	-v,--verbose	switch on diagnostic messages
               	-h,--help	display this message
               -s: Option doesn't exist!
dwifslpreproc: [ERROR] For debugging, inspect contents of scratch directory: /home/sajidhussain/Desktop/mydataset/dwifslpreproc-tmp-HXE56S/
dwifslpreproc: Scratch directory retained; location: /home/sajidhussain/Desktop/mydataset/dwifslpreproc-tmp-HXE56S/

I think the issue is simply a missing ‘-’ in --slm=linear in your -eddy_options. Does that fix it?

I figured out some bugs but after the end, I got this error

dwifslpreproc: [ERROR] Unable to find FSL output file for path “field_map”

Done with the above problem,