Dear MRtrix experts:
Something goes wrong when I run this command :
dwifslpreproc degibbs.mif geomcorr.mif \
-nocleanup -pe_dir AP -rpe_pair -se_epi b0_pair.mif \
-eddy_options " --data is shelled --slm=linear " -force
Before that, I use mrcat to combine the mif file into b0_pair.mif:
dwiextract raw1000AP.mif b0_AP.mif -bzero -force
dwiextract raw1000.mif - -bzero | mrconvert - -coord 3 0 b0_PA.mif -force
mrcat b0_PA.mif b0_AP.mif b0_pair.mif
The error is:
dwifslpreproc:
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: /home/cmet-standard/connectome_test/test_data/dwifslpreproc-tmp-AM7P8S/
Command: mrconvert /home/cmet-standard/connectome_test/test_data/degibbs.mif /home/cmet-standard/connectome_test/test_data/dwifslpreproc-tmp-AM7P8S/dwi.mif -json_export /home/cmet-standard/connectome_test/test_data/dwifslpreproc-tmp-AM7P8S/dwi.json
Command: mrconvert /home/cmet-standard/connectome_test/test_data/b0_pair.mif /home/cmet-standard/connectome_test/test_data/dwifslpreproc-tmp-AM7P8S/se_epi.mif
dwifslpreproc: Changing to scratch directory (/home/cmet-standard/connectome_test/test_data/dwifslpreproc-tmp-AM7P8S/)
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: mrconvert se_epi.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.nii.gz --config=/home/cmet-standard/fsl/etc/flirtsch/b02b0.cnf --verbose
Command: mrconvert dwi.mif -import_pe_table dwi_manual_pe_scheme.txt - | mrinfo - -export_pe_eddy applytopup_config.txt applytopup_indices.txt
Command: mrconvert dwi.mif dwi_pe_0.nii -coord 3 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111 -strides -1,+2,+3,+4 -json_export dwi_pe_0.json
Command: applytopup --imain=dwi_pe_0.nii --datain=applytopup_config.txt --inindex=1 --topup=field --out=dwi_pe_0_applytopup.nii --method=jac
Command: mrconvert dwi_pe_0_applytopup.nii.gz dwi_pe_0_applytopup.mif -json_import dwi_pe_0.json
Command: dwi2mask dwi_pe_0_applytopup.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_cuda10.2 --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --data is shelled --slm=linear --out=dwi_post_eddy --verbose
dwifslpreproc: CUDA version of 'eddy' was not successful; attempting OpenMP version
Command: eddy_cpu --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --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 --topup=field --data is shelled --slm=linear --out=dwi_post_eddy --verbose (app.py:199)
dwifslpreproc: [ERROR] Information from failed command:
dwifslpreproc:
=============
eddy_cuda10.2
=============
========
eddy_cpu
========
=============
eddy_cuda10.2
=============
Part of FSL (ID: "")
eddy
Copyright(c) 2015, University of Oxford (Jesper Andersson)
Usage:
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
--data: Option doesn't exist!
========
eddy_cpu
========
Part of FSL (ID: "")
eddy
Copyright(c) 2015, University of Oxford (Jesper Andersson)
Usage:
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
--data: Option doesn't exist!
dwifslpreproc:
dwifslpreproc: [ERROR] For debugging, inspect contents of scratch directory: /home/cmet-standard/connectome_test/test_data/dwifslpreproc-tmp-AM7P8S/
dwifslpreproc: Scratch directory retained; location: /home/cmet-standard/connectome_test/test_data/dwifslpreproc-tmp-AM7P8S/
Hope some one can help me, I really appreciate it !