XCP-D postprocessing when using fmriprep outputs: ValueError: 'desc' is not a recognized entity

Software Support
1

While running the xcp-d command that uses fmriprep outputs, I ran into an error:
ValueError: 'desc' is not a recognized entity. If you're sure you want to impose this constraint, set invalid_filters='allow'.

The command used was:

docker run --rm -it **\**
-v /home/sja/Projects/fmriusic/Derivatives/fmriprep0305:/fmriprep/:ro **\**
-v /home/sja/Projects/fmriusic/XCP-D/wkdir:/work:rw **\**
-v /home/sja/Projects/fmriusic/XCP-D/sub-05:/out:rw **\**
-v /home/sja/Projects/fmriusic/Derivatives/fmriprep0305/fmriprep-21.0.2/sourcedata/freesurfer:/freesurfer:ro **\**
pennlinc/xcp_d:latest **\**
/fmriprep /out participant **\**
-w /work --smoothing 6 --participant_label 05

Iā€™m unsure if this is an error with my xcp-d command or the fmriprep outputs (I ran version 21.0.2).

Dataset tree:
fmriprep0305
ā””ā”€ā”€ fmriprep-21.0.2
    ā”œā”€ā”€ dataset_description.json
    ā”œā”€ā”€ desc-aparcaseg_dseg.tsv
    ā”œā”€ā”€ desc-aseg_dseg.tsv
    ā”œā”€ā”€ logs
    ā”‚   ā”œā”€ā”€ CITATION.bib
    ā”‚   ā”œā”€ā”€ CITATION.html
    ā”‚   ā”œā”€ā”€ CITATION.md
    ā”‚   ā””ā”€ā”€ CITATION.tex
    ā”œā”€ā”€ sourcedata
    ā”‚   ā””ā”€ā”€ freesurfer
    ā”œā”€ā”€ sub-05
    ā”‚   ā”œā”€ā”€ anat
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_desc-aparcaseg_dseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_desc-aseg_dseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_desc-brain_mask.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_desc-brain_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_desc-preproc_T1w.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_desc-preproc_T1w.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_dseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_from-fsnative_to-T1w_mode-image_xfm.txt
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_from-T1w_to-fsnative_mode-image_xfm.txt
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_hemi-L_inflated.surf.gii
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_hemi-L_midthickness.surf.gii
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_hemi-L_pial.surf.gii
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_hemi-L_smoothwm.surf.gii
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_hemi-R_inflated.surf.gii
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_hemi-R_midthickness.surf.gii
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_hemi-R_pial.surf.gii
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_hemi-R_smoothwm.surf.gii
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_label-CSF_probseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_label-GM_probseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_label-WM_probseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_space-MNI152NLin2009cAsym_desc-brain_mask.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_space-MNI152NLin2009cAsym_dseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
    ā”‚   ā”‚   ā””ā”€ā”€ sub-05_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
    ā”‚   ā”œā”€ā”€ figures
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_desc-about_T1w.html
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_desc-conform_T1w.html
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_desc-reconall_T1w.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_desc-summary_T1w.html
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_dseg.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_run-1_fmapid-auto00002_desc-phasediff_fieldmap.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_run-2_fmapid-auto00003_desc-phasediff_fieldmap.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_space-MNI152NLin2009cAsym_T1w.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_desc-bbregister_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_desc-carpetplot_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_desc-compcorvar_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_desc-confoundcorr_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_desc-rois_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_desc-sdc_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_desc-summary_bold.html
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_desc-validation_bold.html
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_desc-bbregister_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_desc-carpetplot_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_desc-compcorvar_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_desc-confoundcorr_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_desc-rois_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_desc-sdc_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_desc-summary_bold.html
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_desc-validation_bold.html
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_desc-bbregister_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_desc-carpetplot_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_desc-compcorvar_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_desc-confoundcorr_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_desc-rois_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_desc-sdc_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_desc-summary_bold.html
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_desc-validation_bold.html
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_desc-bbregister_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_desc-carpetplot_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_desc-compcorvar_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_desc-confoundcorr_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_desc-rois_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_desc-sdc_bold.svg
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_desc-summary_bold.html
    ā”‚   ā”‚   ā””ā”€ā”€ sub-05_task-sadsh_desc-validation_bold.html
    ā”‚   ā”œā”€ā”€ fmap
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_run-1_fmapid-auto00002_desc-coeff0_fieldmap.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_run-1_fmapid-auto00002_desc-coeff1_fieldmap.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_run-1_fmapid-auto00002_desc-magnitude_fieldmap.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_run-1_fmapid-auto00002_desc-preproc_fieldmap.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_run-1_fmapid-auto00002_desc-preproc_fieldmap.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_run-2_fmapid-auto00003_desc-coeff0_fieldmap.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_run-2_fmapid-auto00003_desc-coeff1_fieldmap.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_run-2_fmapid-auto00003_desc-magnitude_fieldmap.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_run-2_fmapid-auto00003_desc-preproc_fieldmap.json
    ā”‚   ā”‚   ā””ā”€ā”€ sub-05_run-2_fmapid-auto00003_desc-preproc_fieldmap.nii.gz
    ā”‚   ā”œā”€ā”€ func
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_desc-CompCorA_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_desc-CompCorC_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_desc-CompCorT_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_desc-CompCorW_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_desc-confounds_timeseries.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_desc-confounds_timeseries.tsv
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_from-scanner_to-T1w_mode-image_xfm.txt
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_from-T1w_to-scanner_mode-image_xfm.txt
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_space-MNI152NLin2009cAsym_boldref.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_space-MNI152NLin2009cAsym_desc-brain_mask.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_space-MNI152NLin2009cAsym_desc-preproc_bold.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-happy_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_desc-CompCorA_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_desc-CompCorC_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_desc-CompCorT_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_desc-CompCorW_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_desc-confounds_timeseries.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_desc-confounds_timeseries.tsv
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_from-scanner_to-T1w_mode-image_xfm.txt
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_from-T1w_to-scanner_mode-image_xfm.txt
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_desc-CompCorA_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_desc-CompCorC_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_desc-CompCorT_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_desc-CompCorW_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_desc-confounds_timeseries.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_desc-confounds_timeseries.tsv
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_from-scanner_to-T1w_mode-image_xfm.txt
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_from-T1w_to-scanner_mode-image_xfm.txt
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_space-MNI152NLin2009cAsym_boldref.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_space-MNI152NLin2009cAsym_desc-brain_mask.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_space-MNI152NLin2009cAsym_desc-preproc_bold.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadln_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_desc-CompCorA_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_desc-CompCorC_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_desc-CompCorT_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_desc-CompCorW_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_desc-confounds_timeseries.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_desc-confounds_timeseries.tsv
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_from-scanner_to-T1w_mode-image_xfm.txt
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_from-T1w_to-scanner_mode-image_xfm.txt
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_space-MNI152NLin2009cAsym_boldref.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_space-MNI152NLin2009cAsym_desc-brain_mask.json
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
    ā”‚   ā”‚   ā”œā”€ā”€ sub-05_task-sadsh_space-MNI152NLin2009cAsym_desc-preproc_bold.json
    ā”‚   ā”‚   ā””ā”€ā”€ sub-05_task-sadsh_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
    ā”‚   ā””ā”€ā”€ log
    ā”‚       ā”œā”€ā”€ 20221005-023524_94f1fa31-4fe0-4d5c-9b7d-8450d566cd39
    ā”‚       ā”‚   ā””ā”€ā”€ fmriprep.toml
    ā”‚       ā””ā”€ā”€ 20230131-043513_ee4ce804-4fc2-4b50-a3ea-2cb388a1e155
    ā”‚           ā””ā”€ā”€ fmriprep.toml
    ā”œā”€ā”€ sub-05.html
    ā”œā”€ā”€ task-happy_bold.json
    ā”œā”€ā”€ task-rest_bold.json
    ā”œā”€ā”€ task-sadln_bold.json
    ā””ā”€ā”€ task-sadsh_bold.json

XCP-D Version: 0.3.2
Environment: Docker

Please let me know if any other information is needed, and thank you in advance!
Best,
Mounami

2

Hi @Mounami_K and welcome to neurostars!

Looks like you need to pass in /home/sja/Projects/fmriusic/Derivatives/fmriprep0305/fmriprep-21.0.2 as your input directory.

Best,
Steven

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