Fmripost-aroma error: 'res' or 'desc' is not a recognized entity

LawsOfForm · October 24, 2024, 8:49am

Summary of what happened:

Dear NeuroStars community,
Unfortunately, I ran into some error trying fmripost-aroma which I cannot resolve on my own.
I have an error-free BIDS dataset tested with bids-validator@1.14.13 docker version.
After using fmriprep24.1.0 on my BIDS data set I get the recommended 2x2x2 isomorph outputs for my task bold sessions, like

sub-04_ses-01_task-categories_run-01_space-MNI152NLin2009cAsym_res-02_boldref.nii.gz
-sub-04_ses-01_task-categories_run-01_space-MNI152NLin2009cAsym_res-02_desc-preproc_bold.nii.gz

when I run now the fmripost-aroma I get the following errors

ValueError: ‘res’ is not a recognized entity. If you’re sure you want to impose this constraint, set invalid_filters=‘allow’.
or sometimes
ValueError: ‘desc’ is not a recognized entity. If you’re sure you want to impose this constraint, set invalid_filters=‘allow’.

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

# Run the fMRIPost-AROMA analysis
docker run --rm \
    -v $BIDS_DIR:/data:ro \
    -v $OUTPUT_DIR:/out \
    nipreps/fmripost-aroma:latest\
    /data /out participant \
    --participant-label "sub-$SUBJ" \
    --n_cpus 4

Version:

fmripost-aroma v0.0.8
fmriprept v24.1.0
bids-validator@1.14.13

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

I use a docker container, see the script.

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

docker run -ti --rm -v /media/Data03/Studies/VerFlu/VerFlu_BIDS_test:/data:ro bids/validator /data
bids-validator@1.14.13
(node:1) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
	1: [WARN] Not all subjects/sessions/runs have the same scanning parameters. (code: 39 - INCONSISTENT_PARAMETERS)
		./sub-04/ses-01/fmap/sub-04_ses-01_acq-fmap_run-02_magnitude1.nii.gz
		./sub-04/ses-01/fmap/sub-04_ses-01_acq-fmap_run-02_magnitude2.nii.gz
		./sub-04/ses-01/fmap/sub-04_ses-01_acq-fmap_run-02_phasediff.nii.gz
		./sub-04/ses-02/fmap/sub-04_ses-02_acq-fmap_run-02_magnitude1.nii.gz
		./sub-04/ses-02/fmap/sub-04_ses-02_acq-fmap_run-02_magnitude2.nii.gz
		./sub-04/ses-02/fmap/sub-04_ses-02_acq-fmap_run-02_phasediff.nii.gz

	Please visit https://neurostars.org/search?q=INCONSISTENT_PARAMETERS for existing conversations about this issue.

	2: [WARN] Tabular file contains custom columns not described in a data dictionary (code: 82 - CUSTOM_COLUMN_WITHOUT_DESCRIPTION)
		./participants.tsv
			Evidence: Columns: date, age, birhtday, sex not defined, please define in: /participants.json

	Please visit https://neurostars.org/search?q=CUSTOM_COLUMN_WITHOUT_DESCRIPTION for existing conversations about this issue.

	3: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)

	Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.

	4: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered based on the presence of only one author field. Please ignore if all contributors are already properly listed. (code: 102 - TOO_FEW_AUTHORS)

	Please visit https://neurostars.org/search?q=TOO_FEW_AUTHORS for existing conversations about this issue.

        Summary:                  Available Tasks:        Available Modalities: 
        74 Files, 311.75MB        categories              MRI                   
        1 - Subject               rest                                          
        2 - Sessions                                                            


	If you have any questions, please post on https://neurostars.org/tags/bids.

Relevant log outputs (up to 20 lines):

2024-10-24 08:24:37,860 [ WARNING] WARNING: SOCKS support in urllib3 requires the installation of optional dependencies: specifically, PySocks.  For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#socks-proxies
2024-10-24 08:24:39,131 [ WARNING] Telemetry disabled because sentry_sdk is not installed.

...

2024-10-24 08:24:48,539 [IMPORTANT] Building fMRIPost-AROMA's workflow:
           * BIDS dataset path: /data.
           * Participant list: ['04'].
           * Run identifier: 20241024-082437_2b67a9a5-869a-47a4-b832-d9f33c28c33d.
           * Output spaces: None.
...

raise ValueError(msg + "If you're sure you want to impose "
ValueError: 'desc' is not a recognized entity. If you're sure you want to impose this constraint, set invalid_filters='allow'.
fMRIPost-AROMA analysis completed for subject: sub-04

Screenshots / relevant information:

system Ubuntu 20.04.6 LTS

troubleshooting so far:

I tried to run several fmripost-aroma version and also the main, latest and unstable docker implementation but they all showed the same error.
when I try to run the latest fmripost-aroma with the invalid_filters flag --invalid-filters-allow or --invalid-filters = ‘allow’; I get an “unrecognized arguments” error
when I run the code with --skip_bids_validation I get the ‘res’ or ‘desc’ error again.

Any help is highly appreciated.

Steven · October 24, 2024, 1:08pm

Hi @LawsOfForm and welcome to neurostars!

That’s the wrong MNI space, you need --output-spaces MNI152NLin6Asym:res-02 from fmriprep.

Best,
Steven

tsalo · October 24, 2024, 1:27pm

I’ve also seen that desc error when providing a path to a non-BIDS dataset folder or a raw BIDS dataset in the past.

Can you show the tree of $BIDS_DIR?

LawsOfForm · October 25, 2024, 7:28am

Hi Steven,
thanks for your comment. I also tried with --output-spaces MNI152NLin6Asym:res-02 and --output-spaces MNI152NLin6Asym because MNI152NLin6Asym should already have an isotropic 2x2x2 resolution. Then I got the ‘desc’ error.

Best,
Filip

LawsOfForm · October 25, 2024, 8:06am

Hi Tsalo,
thanks for your comment.
the $BIDS_DIR looks like this. (I deleted ses-02 branches and some preprocessing files to be within the limits of allowed number of characters).
Best
Filip

/media/Data03/Studies/VerFlu/VerFlu_BIDS_test
├── participants.tsv
├── dataset_description.json
├── derivatives
│   └── fmriprep
│       ├── logs
│       └── sub-04
│           ├── dataset_description.json
│           ├── desc-aparcaseg_dseg.tsv
│           ├── desc-aseg_dseg.tsv
│           ├── logs
│           │   ├── CITATION.bib
│           │   ├── CITATION.html
│           │   ├── CITATION.md
│           │   └── CITATION.tex
│           ├── sourcedata
│           │   └── freesurfer
│           │       ├── fsaverage
│           │       │   ├── label
...
│           ├── sub-04
│           │   ├── anat
│           │   │   ├── sub-04_desc-brain_mask.json
│           │   │   ├── sub-04_desc-brain_mask.nii.gz
│           │   │   ├── sub-04_desc-preproc_T1w.json
│           │   │   ├── sub-04_desc-preproc_T1w.nii.gz
│           │   │   ├── sub-04_desc-preproc_T2w.json
│           │   │   ├── sub-04_desc-preproc_T2w.nii.gz
│           │   │   ├── sub-04_desc-ribbon_mask.json
│           │   │   ├── sub-04_desc-ribbon_mask.nii.gz
│           │   │   ├── sub-04_dseg.nii.gz
│           │   │   ├── sub-04_from-fsnative_to-T1w_mode-image_xfm.txt
│           │   │   ├── sub-04_from-MNI152NLin2009cAsym_to-T1w_mode-
...
brain_mask.json
│           │   │   ├── sub-04_space-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz
│           │   │   ├── sub-04_space-MNI152NLin2009cAsym_res-02_desc-preproc_T1w.json
│           │   │   ├── sub-04_space-MNI152NLin2009cAsym_res-02_desc-preproc_T1w.nii.gz
│           │   │   ├── sub-04_space-MNI152NLin2009cAsym_res-02_dseg.json
│           │   │   ├── sub-04_space-MNI152NLin2009cAsym_res-02_dseg.nii.gz
│           │   │   ├── sub-04_space-MNI152NLin2009cAsym_res-02_label-CSF_probseg.nii.gz
│           │   │   ├── sub-04_space-MNI152NLin2009cAsym_res-02_label-GM_probseg.nii.gz
│           │   │   ├── sub-04_space-MNI152NLin2009cAsym_res-02_label-WM_probseg.nii.gz
│           │   │   ├── sub-04_space-MNI152NLin6Asym_desc-brain_mask.json
│           │   │   ├── sub-04_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
│           │   │   ├── sub-04_space-MNI152NLin6Asym_desc-preproc_T1w.json
│           │   │   ├── sub-04_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz
│           │   │   ├── sub-04_space-MNI152NLin6Asym_dseg.nii.gz
│           │   │   ├── sub-04_space-MNI152NLin6Asym_label-CSF_probseg.nii.gz
│           │   │   ├── sub-04_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
│           │   │   └── sub-04_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
│           │   ├── figures
│           │   │   ├── sub-04_desc-conform_T1w.html
│           │   │   ├── sub-04_desc-reconall_T1w.svg
│           │   │   ├── sub-04_dseg.svg
│           │   │   ├── sub-04_ses-01_acq-fmap_run-01_fmapid-auto00000_desc-phasediff_fieldmap.svg
│           │   │   ├── sub-04_ses-01_acq-fmap_run-02_fmapid-auto00001_desc-phasediff_fieldmap.svg
│           │   │   ├── sub-04_ses-01_desc-about_T1w.html
│           │   │   ├── sub-04_ses-01_desc-summary_T1w.html
│           │   │   ├── sub-04_ses-01_task-categories_run-01_desc-carpetplot_bold.svg
│           │   │   ├── sub-04_ses-01_task-categories_run-01_desc-compcorvar_bold.svg
│           │   │   ├── sub-04_ses-01_task-categories_run-01_desc-confoundcorr_bold.svg
│           │   │   ├── sub-04_ses-01_task-categories_run-01_desc-coreg_bold.svg
│           │   │   ├── sub-04_ses-01_task-categories_run-01_desc-fmapCoreg_bold.svg
│           │   │   ├── sub-04_ses-01_task-categories_run-01_desc-rois_bold.svg
│           │   │   ├── sub-04_ses-01_task-categories_run-01_desc-sdc_bold.svg
│           │   │   ├── sub-04_ses-01_task-categories_run-01_desc-summary_bold.html
│           │   │   ├── sub-04_ses-01_task-categories_run-01_desc-validation_bold.html
│           │   │   ├── sub-04_ses-01_task-categories_run-02_desc-carpetplot_bold.svg
│           │   │   ├── sub-04_ses-01_task-categories_run-02_desc-compcorvar_bold.svg
│           │   │   ├── sub-04_ses-01_task-categories_run-02_desc-confoundcorr_bold.svg
│           │   │   ├── sub-04_ses-01_task-categories_run-02_desc-coreg_bold.svg
│           │   │   ├── sub-04_ses-01_task-categories_run-02_desc-fmapCoreg_bold.svg
│           │   │   ├── sub-04_ses-01_task-categories_run-02_desc-rois_bold.svg
│           │   │   ├── sub-04_ses-01_task-categories_run-02_desc-sdc_bold.svg
│           │   │   ├── sub-04_ses-01_task-categories_run-02_desc-summary_bold.html
│           │   │   ├── sub-04_ses-01_task-categories_run-02_desc-validation_bold.html
│           │   │   ├── sub-04_ses-01_task-rest_desc-carpetplot_bold.svg
│           │   │   ├── sub-04_ses-01_task-rest_desc-compcorvar_bold.svg
│           │   │   ├── sub-04_ses-01_task-rest_desc-confoundcorr_bold.svg
│           │   │   ├── sub-04_ses-01_task-rest_desc-coreg_bold.svg
│           │   │   ├── sub-04_ses-01_task-rest_desc-fmapCoreg_bold.svg
│           │   │   ├── sub-04_ses-01_task-rest_desc-rois_bold.svg
│           │   │   ├── sub-04_ses-01_task-rest_desc-sdc_bold.svg
│           │   │   ├── sub-04_ses-01_task-rest_desc-summary_bold.html
│           │   │   ├── sub-04_ses-01_task-rest_desc-validation_bold.html
│           │   ├── ses-01
│           │   │   ├── anat
│           │   │   │   ├── sub-04_ses-01_acq-electrodes_from-orig_to-T1w_mode-image_xfm.txt
│           │   │   │   └── sub-04_ses-01_acq-noelectrodes_from-orig_to-T1w_mode-image_xfm.txt
│           │   │   ├── fmap
│           │   │   │   ├── sub-04_ses-01_acq-fmap_run-01_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
│           │   │   │   ├── sub-04_ses-01_acq-fmap_run-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
│           │   │   │   ├── sub-04_ses-01_acq-fmap_run-01_fmapid-auto00000_desc-preproc_fieldmap.json
│           │   │   │   ├── sub-04_ses-01_acq-fmap_run-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
│           │   │   │   ├── sub-04_ses-01_acq-fmap_run-02_fmapid-auto00001_desc-coeff_fieldmap.nii.gz
│           │   │   │   ├── sub-04_ses-01_acq-fmap_run-02_fmapid-auto00001_desc-magnitude_fieldmap.nii.gz
│           │   │   │   ├── sub-04_ses-01_acq-fmap_run-02_fmapid-auto00001_desc-preproc_fieldmap.json
│           │   │   │   └── sub-04_ses-01_acq-fmap_run-02_fmapid-auto00001_desc-preproc_fieldmap.nii.gz
│           │   │   └── func
│           │   │       ├── sub-04_ses-01_task-categories_run-01_desc-brain_mask.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_desc-brain_mask.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-01_desc-confounds_timeseries.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_desc-confounds_timeseries.tsv
│           │   │       ├── sub-04_ses-01_task-categories_run-01_desc-coreg_boldref.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_desc-coreg_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-01_desc-hmc_boldref.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_desc-hmc_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-01_from-boldref_to-auto00000_mode-image_xfm.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_from-boldref_to-auto00000_mode-image_xfm.txt
│           │   │       ├── sub-04_ses-01_task-categories_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│           │   │       ├── sub-04_ses-01_task-categories_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-MNI152NLin2009cAsym_res-02_boldref.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-MNI152NLin2009cAsym_res-02_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-MNI152NLin2009cAsym_res-02_desc-brain_mask.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-MNI152NLin2009cAsym_res-02_desc-preproc_bold.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-MNI152NLin2009cAsym_res-02_desc-preproc_bold.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-MNI152NLin6Asym_boldref.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-MNI152NLin6Asym_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-MNI152NLin6Asym_desc-brain_mask.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-MNI152NLin6Asym_desc-preproc_bold.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-T1w_boldref.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-T1w_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-T1w_desc-brain_mask.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-T1w_desc-brain_mask.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-T1w_desc-preproc_bold.json
│           │   │       ├── sub-04_ses-01_task-categories_run-01_space-T1w_desc-preproc_bold.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-02_desc-brain_mask.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_desc-brain_mask.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-02_desc-confounds_timeseries.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_desc-confounds_timeseries.tsv
│           │   │       ├── sub-04_ses-01_task-categories_run-02_desc-coreg_boldref.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_desc-coreg_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-02_desc-hmc_boldref.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_desc-hmc_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-02_from-boldref_to-auto00000_mode-image_xfm.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_from-boldref_to-auto00000_mode-image_xfm.txt
│           │   │       ├── sub-04_ses-01_task-categories_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│           │   │       ├── sub-04_ses-01_task-categories_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-MNI152NLin2009cAsym_res-02_boldref.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-MNI152NLin2009cAsym_res-02_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-MNI152NLin2009cAsym_res-02_desc-brain_mask.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-MNI152NLin2009cAsym_res-02_desc-preproc_bold.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-MNI152NLin2009cAsym_res-02_desc-preproc_bold.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-MNI152NLin6Asym_boldref.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-MNI152NLin6Asym_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-MNI152NLin6Asym_desc-brain_mask.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-MNI152NLin6Asym_desc-preproc_bold.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-T1w_boldref.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-T1w_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-T1w_desc-brain_mask.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-T1w_desc-brain_mask.nii.gz
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-T1w_desc-preproc_bold.json
│           │   │       ├── sub-04_ses-01_task-categories_run-02_space-T1w_desc-preproc_bold.nii.gz
│           │   │       ├── sub-04_ses-01_task-rest_desc-brain_mask.json
│           │   │       ├── sub-04_ses-01_task-rest_desc-brain_mask.nii.gz
│           │   │       ├── sub-04_ses-01_task-rest_desc-confounds_timeseries.json
│           │   │       ├── sub-04_ses-01_task-rest_desc-confounds_timeseries.tsv
│           │   │       ├── sub-04_ses-01_task-rest_desc-coreg_boldref.json
│           │   │       ├── sub-04_ses-01_task-rest_desc-coreg_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-rest_desc-hmc_boldref.json
│           │   │       ├── sub-04_ses-01_task-rest_desc-hmc_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-rest_from-boldref_to-auto00001_mode-image_xfm.json
│           │   │       ├── sub-04_ses-01_task-rest_from-boldref_to-auto00001_mode-image_xfm.txt
│           │   │       ├── sub-04_ses-01_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│           │   │       ├── sub-04_ses-01_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│           │   │       ├── sub-04_ses-01_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│           │   │       ├── sub-04_ses-01_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│           │   │       ├── sub-04_ses-01_task-rest_space-MNI152NLin2009cAsym_res-02_boldref.json
│           │   │       ├── sub-04_ses-01_task-rest_space-MNI152NLin2009cAsym_res-02_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-rest_space-MNI152NLin2009cAsym_res-02_desc-brain_mask.json
│           │   │       ├── sub-04_ses-01_task-rest_space-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz
│           │   │       ├── sub-04_ses-01_task-rest_space-MNI152NLin2009cAsym_res-02_desc-preproc_bold.json
│           │   │       ├── sub-04_ses-01_task-rest_space-MNI152NLin2009cAsym_res-02_desc-preproc_bold.nii.gz
│           │   │       ├── sub-04_ses-01_task-rest_space-MNI152NLin6Asym_boldref.json
│           │   │       ├── sub-04_ses-01_task-rest_space-MNI152NLin6Asym_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-rest_space-MNI152NLin6Asym_desc-brain_mask.json
│           │   │       ├── sub-04_ses-01_task-rest_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
│           │   │       ├── sub-04_ses-01_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.json
│           │   │       ├── sub-04_ses-01_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
│           │   │       ├── sub-04_ses-01_task-rest_space-T1w_boldref.json
│           │   │       ├── sub-04_ses-01_task-rest_space-T1w_boldref.nii.gz
│           │   │       ├── sub-04_ses-01_task-rest_space-T1w_desc-brain_mask.json
│           │   │       ├── sub-04_ses-01_task-rest_space-T1w_desc-brain_mask.nii.gz
│           │   │       ├── sub-04_ses-01_task-rest_space-T1w_desc-preproc_bold.json
│           │   │       └── sub-04_ses-01_task-rest_space-T1w_desc-

└── sub-04
    ├── ses-01
    │   ├── anat
    │   │   ├── sub-04_ses-01_acq-electrodes_T1w.json
    │   │   ├── sub-04_ses-01_acq-electrodes_T1w.nii.gz
    │   │   ├── sub-04_ses-01_acq-noelectrodes_T1w.json
    │   │   ├── sub-04_ses-01_acq-noelectrodes_T1w.nii.gz
    │   │   ├── sub-04_ses-01_T2w.json
    │   │   └── sub-04_ses-01_T2w.nii.gz
    │   ├── dwi
    │   │   ├── sub-04_ses-01_dwi.bval
    │   │   ├── sub-04_ses-01_dwi.bvec
    │   │   ├── sub-04_ses-01_dwi.json
    │   │   └── sub-04_ses-01_dwi.nii.gz
    │   ├── fmap
    │   │   ├── sub-04_ses-01_acq-fmap_run-01_magnitude1.json
    │   │   ├── sub-04_ses-01_acq-fmap_run-01_magnitude1.nii.gz
    │   │   ├── sub-04_ses-01_acq-fmap_run-01_magnitude2.json
    │   │   ├── sub-04_ses-01_acq-fmap_run-01_magnitude2.nii.gz
    │   │   ├── sub-04_ses-01_acq-fmap_run-01_phasediff.json
    │   │   ├── sub-04_ses-01_acq-fmap_run-01_phasediff.nii.gz
    │   │   ├── sub-04_ses-01_acq-fmap_run-02_magnitude1.json
    │   │   ├── sub-04_ses-01_acq-fmap_run-02_magnitude1.nii.gz
    │   │   ├── sub-04_ses-01_acq-fmap_run-02_magnitude2.json
    │   │   ├── sub-04_ses-01_acq-fmap_run-02_magnitude2.nii.gz
    │   │   ├── sub-04_ses-01_acq-fmap_run-02_phasediff.json
    │   │   ├── sub-04_ses-01_acq-fmap_run-02_phasediff.nii.gz
    │   │   ├── sub-04_ses-01_dir-LR_run-1_epi.json
    │   │   ├── sub-04_ses-01_dir-LR_run-1_epi.nii.gz
    │   │   ├── sub-04_ses-01_dir-RL_run-1_epi.json
    │   │   ├── sub-04_ses-01_dir-RL_run-1_epi.nii.gz
    │   │   ├── sub-04_ses-01_dir-RL_run-2_epi.json
    │   │   └── sub-04_ses-01_dir-RL_run-2_epi.nii.gz
    │   └── func
    │       ├── sub-04_ses-01_task-categories_run-01_bold.json
    │       ├── sub-04_ses-01_task-categories_run-01_bold.nii.gz
    │       ├── sub-04_ses-01_task-categories_run-01_events.tsv
    │       ├── sub-04_ses-01_task-categories_run-02_bold.json
    │       ├── sub-04_ses-01_task-categories_run-02_bold.nii.gz
    │       ├── sub-04_ses-01_task-categories_run-02_events.tsv
    │       ├── sub-04_ses-01_task-rest_bold.json
    │       └── sub-04_ses-01_task-rest_bold.nii.gz

tsalo · October 25, 2024, 12:30pm

It looks like your BIDS_DIR is a raw dataset with the fMRIPrep derivatives organized within it. With fMRIPost-AROMA you need to provide the paths to the raw dataset and the fMRIPrep derivatives separately. So instead of:

fmripost-aroma /data /out participant

you would either directly pass in the fMRIPrep derivatives without the raw dataset:

fmripost-aroma /data/derivatives/fmriprep /out participant

Or pass in both as separate arguments:

fmripost-aroma /data /out participant --derivatives fmriprep=/data/derivatives/fmriprep

LawsOfForm · October 28, 2024, 8:33am

You found the error thanks, now it’s working.
As a minor detail, solution 2 worked but not solution 1, so the final working code is

docker run --rm
-v $BIDS_DIR:/data:ro
-v $OUTPUT_DIR:/out
nipreps/fmripost-aroma:latest
/data /out participant
–derivatives fmriprep=/data/derivatives/fmriprep
–participant-label “sub-$SUBJ”
–n_cpus 4

Best, Filip

tsalo · October 28, 2024, 1:17pm

Solution 1 should work. Any chance you could share the traceback from when you attempted it?