QC output file missing after running QSIPrep

Software Support
1

Continuing the discussion from Ringing in FA images after TBSS registration:

Summary of what happened:

Hi @Steven,
QSIPrep run without errors apparently (no SLURM .out/.err files) but the QC files are missing. Here is the requested info on the QSIPrep command used and the tree directory structure for one of my subjects.

Thank you for your help!

Command used (and if a helper script was used, a link to the helper script or the command generated):

for i in $(seq -w ); do
  subject=sub-${i}
docker run -ti --rm \
  -v /path/output_dcm2bids:/data:ro \
  -v /path/QSIPrep/qsiprep_output_dir:/out \
  -v /path/QSIPrep/qsiprep_work_dir:/work \
  -v /softwares/freesurfer-6.0.0/license.txt:/license.txt \
  pennlinc/qsiprep:latest \
  /data /out participant \
  --skip-bids-validation \
  --participant-label ${subject#sub-} \
  --anat-modality T1w \
  --unringing-method mrdegibbs \
  --distortion-group-merge none \
  --b1-biascorrect-stage none \
  --separate-all-dwis \
  --output-resolution 2 \
  --fs-license-file /license.txt \
  --hmc-model eddy \
  --work-dir /work/sub-${subject#sub-} \
  --write-graph \
  --notrack 
  
done

Version:

1.0.2

Environment (Docker, Singularity / Apptainer, custom installation):

Docker

Data formatted according to a validatable standard? Please provide the output of the validator:

BIDS standard

Screenshots / relevant information:

Here is what the tree directory structure of one subject’s QSIPrep outputs

.
├── anat
│   ├── sub-01_from-ACPC_to-anat_mode-image_xfm.mat
│   ├── sub-01_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5
│   ├── sub-01_from-anat_to-ACPC_mode-image_xfm.mat
│   ├── sub-01_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5
│   ├── sub-01_from-orig_to-anat_mode-image_xfm.txt
│   ├── sub-01_space-ACPC_desc-aseg_dseg.nii.gz
│   ├── sub-01_space-ACPC_desc-brain_mask.nii.gz
│   ├── sub-01_space-ACPC_desc-preproc_T1w.json
│   ├── sub-01_space-ACPC_desc-preproc_T1w.nii.gz
│   └── sub-01_space-ACPC_dseg.nii.gz
├── dwi
│   ├── sub-01_desc-confounds_timeseries.tsv
│   ├── sub-01_space-ACPC_desc-brain_mask.nii.gz
│   ├── sub-01_space-ACPC_desc-image_qc.tsv
│   ├── sub-01_space-ACPC_desc-preproc_dwi.b
│   ├── sub-01_space-ACPC_desc-preproc_dwi.b_table.txt
│   ├── sub-01_space-ACPC_desc-preproc_dwi.bval
│   ├── sub-01_space-ACPC_desc-preproc_dwi.bvec
│   ├── sub-01_space-ACPC_desc-preproc_dwi.json
│   ├── sub-01_space-ACPC_desc-preproc_dwi.nii.gz
│   ├── sub-01_space-ACPC_desc-slice_qc.json
│   ├── sub-01_space-ACPC_dwiref.nii.gz
│   ├── sub-01_space-ACPC_model-eddy_stat-cnr_dwimap.json
│   └── sub-01_space-ACPC_model-eddy_stat-cnr_dwimap.nii.gz
├── figures
│   ├── sub-01_about.html
│   ├── sub-01_conform.html
│   ├── sub-01_desc-brainmask_fieldmap.svg
│   ├── sub-01_desc-carpetplot_dwi.svg
│   ├── sub-01_desc-coreg_dwi.svg
│   ├── sub-01_desc-denoising_dwi.svg
│   ├── sub-01_desc-resampled_b0ref.svg
│   ├── sub-01_desc-samplingscheme_dwi.gif
│   ├── sub-01_desc-sdc_b0.svg
│   ├── sub-01_desc-seg_mask.svg
│   ├── sub-01_desc-summary_dwi.html
│   ├── sub-01_desc-unringing_dwi.svg
│   ├── sub-01_fmapreg.svg
│   ├── sub-01_fmapregvsm.svg
│   ├── sub-01_summary.html
│   └── sub-01_t1w2mni.svg
└── log
    └── 20251203-153653_9ec5b9d4-fd49-4670-88ef-57f01ac48012
        └── qsiprep.toml

5 directories, 40 files
2

Hi @jruizfdez,

That^

Best,
Steven

1 Like