Hi,
I am using qsiprep for analyzing neonatal data with the following command:
SINGULARITY_TMPDIR=$PWD SINGULARITY_CACHEDIR=$PWD singularity run --nv -C -B /EBC:/EBC,$PWD:/opt/templateflow /EBC/home/mblesa/qsiprep-0.18.0.sif $PWD $PWD/sub-${BASENAME}_qsiprep participant --participant-label ${BASENAME} -w $PWD --skip-odf-reports --nthreads 16 --omp-nthreads 16 --fs-license-file /EBC/local/infantFS/freesurfer/license.txt --dwi-denoise-window 7 --unringing-method mrdegibbs --output-resolution 1.5 --eddy-config $PWD/eddy_params.json --dwi-only --infant --stop-on-first-crash --skip_bids_validation #> sub-${BASENAME}_qsiprep/log_QSIprep_sub-${BASENAME}.txt
It runs perfectly, without errors and the report looks great. However, when I open the final image sub-8035_ses-01_space-T1w_desc-preproc_dwi.nii.gz it looks like the raw image, no corrections have been applied:
I am sure that I’m missing something really evident, but I can not get my head around it. Any clue? Thanks in advance.
Best regards,
Manuel