Hello everyone!
I have preprocessed my diffusion data using the dwifslpreproc command with MRtrix. However, I received the following warning:
dwifslpreproc: [WARNING] Error running automated EddyQC tool ‘eddy_quad’; QC data written to “[path]” will be files from “eddy” only
The exact same command worked for a previous dataset, successfully generating the eddy_QC report. This time, I receive the same output files in my subject folder, except for the additional eddy folder that should include the actual report files.
A similar problem was reported here: Issue with eddy_qc full output
For my command, I tried to remove the " -scratch" option but the problem remained.
This is my command:
{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−−cnrmaps" \
-nthreads {NTHREADS}
-eddyqc_all ${OUTPUT_DIR}
Anyone knows what could cause this error?
I very much appreciate your help!
Thank you,
Anna
M.Sc. Anna Kwiatkowski
PhD Candidate
Dep. of Psychiatry, Psychotherapy and Psychosomatics
Tel.: +49 241 8037877