Issue with eddy_qc full output

1

Hello, I am running the following on some multi shell data

dwifslpreproc -force dwi_denoised_unringed.mif dwi_prep.mif -rpe_pair -se_epi b0_pair.mif -nocleanup -pe_dir ap -align_seepi -eddyqc_text edd_qc -eddy_options " --data_is_shelled --repol --slm=linear"

and for a large number of subjects eddy runs without error however, the eddy_qc command is failing and giving me the following error.


dwifslpreproc: [WARNING] Error running automated EddyQC tool 'eddy_quad'; QC data written to "/Users/pniresearch/Downloads/NFL/analysis/NFL023/edd_qc" will be files from "eddy" only

*Command:* mrconvert dwi_post_eddy.nii.gz result.mif -coord 2 0:62 -strides -1,3,4,2 -fslgrad dwi_post_eddy.eddy_rotated_bvecs bvals```

Any ideas why this might be?
2

This issue was resolved by removing the -nocleanup flag. It seems that maybe that command was interfering with some of the file dependencies required for eddy_qc?

3

Hello,
I am running into a similar problem when running dwifslpreproc:

{MRTRIXPATH}/dwifslpreproc {FORCE} {OUTPUT_DIR}/{DWI_MIF/%.mif}_den_unr.mif
{OUTPUT_DIR}/{MID}_preproc.mif
-scratch {OUTPUT_DIR}/{MID}
-rpe_none
-pe_dir {PEDIR} \ -eddy_options " --repol --cnr_maps" \ -nthreads {NTHREADS}
-eddyqc_all ${OUTPUT_DIR}

I am receiving the following error:
dwifslpreproc: [WARNING] Error running automated EddyQC tool ‘eddy_quad’; QC data written to “[path]” will be files from “eddy” only

Anyone know where this error might come from?

I would be very grateful for any help! Thanks!
Anna