Error from dwipreproc

1

Hi,
I am using the dwipreproc method to handle motion and distortion correction for DWI data. However, I got an error:

dwipreproc: 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.
dwipreproc: 
dwipreproc: Generated temporary directory: /home/siying/dwipreproc-tmp-EBXVYY/
Command:  mrconvert /home/siying/sharefolder/study/001_control/unring.mif /home/siying/dwipreproc-tmp-EBXVYY/dwi.mif
dwipreproc: Changing to temporary directory (/home/siying/dwipreproc-tmp-EBXVYY/)
Command:  dirstat dwi.mif -output asym
dwipreproc: 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 --out=dwi_post_eddy
dwipreproc: * [WARNING] Command failed: eddy_cuda --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --out=dwi_post_eddy
* dwipreproc: [WARNING] CUDA version of eddy appears to have failed; trying 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 --out=dwi_post_eddy
* dwipreproc: 
* dwipreproc: [ERROR] Command failed: eddy_openmp --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --out=dwi_post_eddy (dwipreproc:853)
* dwipreproc: Output of failed command:
dwipreproc: 
dwipreproc: Changing back to original directory (/home/siying)
dwipreproc: Script failed while executing the command: eddy_openmp --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --out=dwi_post_eddy
dwipreproc: For debugging, inspect contents of temporary directory: /home/siying/dwipreproc-tmp-EBXVYY/
2

Hi @ZWM,

Unfortunately eddy is failing without providing any kind of terminal text output. This makes it almost impossible to diagnose what the issue may be. I would suggest trying to process an example dataset by interacting with the FSL commands directly rather than going through dwipreproc. If you can isolate and reproduce a fault that is entirely independent of any data manipulation by MRtrix3, this is something to be reported to the FSL developers.

Rob

3

Thanks for your suggestion