fMRIPost-AROMA - ValueError: 'bold' is not a recognized entity

Maurice_Pasternak · February 11, 2025, 2:10am

Summary of what happened:

Using fMRIPost-AROMA while providing a raw dataset (this pipeline does not work with a derivatives dataset like fMRIPrep being input). Get the error in the title when attempting to run a subset of sessions.

Firstly, the bids_filter file in question:

{
	"bold": {
		"datatype": "func",
		"session": ["V11"],
		"task": ["rest"],
		"suffix": "bold"
	}
}

tree output:

Permissions Size User Date Modified Name
drwxrwxrwx     - root 10 Feb 20:46   .
.rwxrwxrwx    19 root 13 Nov  2024  ├──  .bidsignore
.rwxrwxrwx   174 root 12 Sep  2024  ├──  dataset_description.json
drwxrwxrwx     - root 10 Feb 20:45  ├──  derivatives
drwxrwxrwx     - root 10 Feb 20:45  │   ├──  aroma
.rwxrwxrwx   104 root  2 Feb 22:58  │   │   ├──  .bidsignore
.rwxrwxrwx   713 root 28 Jan 23:39  │   │   ├──  dataset_description.json
drwxrwxrwx     - root 29 Jan 01:49  │   │   └──  sub-C9ORF364
drwxrwxrwx     - root 29 Jan 01:48  │   │       ├──  log
drwxrwxrwx     - root 29 Jan 02:05  │   │       │   └──  20250129-014656_8af09c25-50bd-4e6c-b748-359af780223c
.rwxrwxrwx  5.7k root 29 Jan 02:05  │   │       │       ├──  crash-20250129-020502-fmripost_aroma-ds_aroma_confounds-dd48ace2-5887-4249-a21c-85d886efa90e.txt
.rwxrwxrwx  1.6k root 29 Jan 01:48  │   │       │       └──  fmripost_aroma.toml
drwxrwxrwx     - root 29 Jan 02:03  │   │       ├──  ses-V11
drwxrwxrwx     - root 29 Jan 02:05  │   │       │   ├──  figures
.rwxrwxrwx   437 root 29 Jan 01:49  │   │       │   │   ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-about_bold.html
.rwxrwxrwx  2.7M root 29 Jan 02:05  │   │       │   │   ├── 󰕙 sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-aroma_bold.svg
.rwxrwxrwx  131k root 29 Jan 02:05  │   │       │   │   ├── 󰕙 sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-metrics_bold.svg
.rwxrwxrwx  664k root 29 Jan 02:05  │   │       │   │   ├── 󰕙 sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-normalization_bold.svg
.rwxrwxrwx   251 root 29 Jan 01:49  │   │       │   │   └──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-summary_bold.html
drwxrwxrwx     - root 10 Feb 20:33  │   │       │   └──  func
.rwxrwxrwx  3.4k root 29 Jan 02:05  │   │       │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-aroma_metrics.json
.rwxrwxrwx  4.2k root 29 Jan 02:05  │   │       │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-aroma_metrics.tsv
.rwxrwxrwx   31M root 29 Jan 02:03  │   │       │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-melodic_components.nii.gz
.rwxrwxrwx  173k root 29 Jan 02:05  │   │       │       └──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_res-2_desc-melodic_mixing.tsv
drwxrwxrwx     - root 29 Jan 01:58  │   │       └──  ses-V12
drwxrwxrwx     - root 29 Jan 02:00  │   │           ├──  figures
.rwxrwxrwx  1.8M root 29 Jan 02:05  │   │           │   ├── 󰕙 sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-aroma_bold.svg
.rwxrwxrwx  156k root 29 Jan 02:05  │   │           │   ├── 󰕙 sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-metrics_bold.svg
.rwxrwxrwx  654k root 29 Jan 02:05  │   │           │   └── 󰕙 sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-normalization_bold.svg
drwxrwxrwx     - root 29 Jan 01:59  │   │           └──  func
.rwxrwxrwx  3.4k root 29 Jan 01:59  │   │               ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-aroma_metrics.json
.rwxrwxrwx  2.9k root 29 Jan 01:59  │   │               ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-aroma_metrics.tsv
.rwxrwxrwx   26k root 29 Jan 01:59  │   │               ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-aroma_timeseries.tsv
.rwxrwxrwx   21M root 29 Jan 01:58  │   │               ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-melodic_components.nii.gz
.rwxrwxrwx  117k root 29 Jan 01:59  │   │               └──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_res-2_desc-melodic_mixing.tsv
drwxrwxrwx     - root 10 Feb 20:46  │   └──  fmriprep
drwxrwxrwx     - root 12 Jan 04:42  │       └──  sub-C9ORF364
drwxrwxrwx     - root 25 Jan 15:41  │           ├──  anat
.rwxrwxrwx   221 root 25 Jan 14:34  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_desc-brain_mask.json
.rwxrwxrwx   52k root 25 Jan 14:34  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_desc-brain_mask.nii.gz
.rwxrwxrwx    28 root 25 Jan 14:32  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_desc-preproc_T1w.json
.rwxrwxrwx   42M root 25 Jan 14:32  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_desc-preproc_T1w.nii.gz
.rwxrwxrwx   219 root 25 Jan 14:35  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_desc-ribbon_mask.json
.rwxrwxrwx  139k root 25 Jan 14:35  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_desc-ribbon_mask.nii.gz
.rwxrwxrwx  238k root 25 Jan 14:37  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_dseg.nii.gz
.rwxrwxrwx   225 root 25 Jan 14:02  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_from-fsnative_to-T1w_mode-image_xfm.txt
.rwxrwxrwx   75M root 25 Jan 15:38  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
.rwxrwxrwx   90M root 25 Jan 15:38  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
.rwxrwxrwx   228 root 25 Jan 14:02  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_from-T1w_to-fsnative_mode-image_xfm.txt
.rwxrwxrwx   75M root 25 Jan 15:38  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
.rwxrwxrwx   90M root 25 Jan 15:38  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
.rwxrwxrwx  5.4M root 25 Jan 14:33  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-L_midthickness.surf.gii
.rwxrwxrwx  5.4M root 25 Jan 14:33  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-L_pial.surf.gii
.rwxrwxrwx  5.4M root 25 Jan 14:33  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-L_space-fsaverage_desc-reg_sphere.surf.gii
.rwxrwxrwx  5.4M root 25 Jan 15:40  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
.rwxrwxrwx  5.4M root 25 Jan 14:34  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
.rwxrwxrwx  5.4M root 25 Jan 14:33  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-L_sphere.surf.gii
.rwxrwxrwx  781k root 25 Jan 14:33  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-L_sulc.shape.gii
.rwxrwxrwx  708k root 25 Jan 14:33  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-L_thickness.shape.gii
.rwxrwxrwx  5.4M root 25 Jan 14:33  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-L_white.surf.gii
.rwxrwxrwx  5.2M root 25 Jan 14:33  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-R_midthickness.surf.gii
.rwxrwxrwx  5.2M root 25 Jan 14:33  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-R_pial.surf.gii
.rwxrwxrwx  5.2M root 25 Jan 14:33  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii
.rwxrwxrwx  5.2M root 25 Jan 15:40  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
.rwxrwxrwx  5.2M root 25 Jan 14:34  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
.rwxrwxrwx  5.2M root 25 Jan 14:33  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-R_sphere.surf.gii
.rwxrwxrwx  764k root 25 Jan 14:33  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-R_sulc.shape.gii
.rwxrwxrwx  691k root 25 Jan 14:33  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-R_thickness.shape.gii
.rwxrwxrwx  5.2M root 25 Jan 14:33  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_hemi-R_white.surf.gii
.rwxrwxrwx  585k root 25 Jan 14:37  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_label-CSF_probseg.nii.gz
.rwxrwxrwx  1.1M root 25 Jan 14:37  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_label-GM_probseg.nii.gz
.rwxrwxrwx  631k root 25 Jan 14:37  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_label-WM_probseg.nii.gz
.rwxrwxrwx  579k root 25 Jan 15:41  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-fsLR_den-91k_curv.dscalar.nii
.rwxrwxrwx   425 root 25 Jan 15:41  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-fsLR_den-91k_curv.json
.rwxrwxrwx  579k root 25 Jan 15:41  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-fsLR_den-91k_sulc.dscalar.nii
.rwxrwxrwx   425 root 25 Jan 15:41  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-fsLR_den-91k_sulc.json
.rwxrwxrwx  579k root 25 Jan 15:41  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-fsLR_den-91k_thickness.dscalar.nii
.rwxrwxrwx   425 root 25 Jan 15:41  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-fsLR_den-91k_thickness.json
.rwxrwxrwx   116 root 25 Jan 15:39  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
.rwxrwxrwx   11k root 25 Jan 15:39  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
.rwxrwxrwx   122 root 25 Jan 15:38  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.json
.rwxrwxrwx  1.0M root 25 Jan 15:38  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
.rwxrwxrwx    97 root 25 Jan 15:39  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin6Asym_res-2_dseg.json
.rwxrwxrwx   51k root 25 Jan 15:39  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin6Asym_res-2_dseg.nii.gz
.rwxrwxrwx  572k root 25 Jan 15:39  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin6Asym_res-2_label-CSF_probseg.nii.gz
.rwxrwxrwx  799k root 25 Jan 15:39  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin6Asym_res-2_label-GM_probseg.nii.gz
.rwxrwxrwx  633k root 25 Jan 15:39  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin6Asym_res-2_label-WM_probseg.nii.gz
.rwxrwxrwx    21 root 25 Jan 15:40  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin2009cAsym_desc-brain_mask.json
.rwxrwxrwx   47k root 25 Jan 15:40  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
.rwxrwxrwx    27 root 25 Jan 15:39  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
.rwxrwxrwx  6.2M root 25 Jan 15:39  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
.rwxrwxrwx  216k root 25 Jan 15:40  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin2009cAsym_dseg.nii.gz
.rwxrwxrwx  3.4M root 25 Jan 15:39  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
.rwxrwxrwx  4.8M root 25 Jan 15:39  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
.rwxrwxrwx  3.8M root 25 Jan 15:39  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
.rwxrwxrwx    28 root 25 Jan 14:38  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT2_desc-preproc_T2w.json
.rwxrwxrwx   39M root 25 Jan 14:38  │           │   └──  sub-C9ORF364_acq-Philips3T3DT2_desc-preproc_T2w.nii.gz
drwxrwxrwx     - root 25 Jan 15:43  │           ├──  figures
.rwxrwxrwx   284 root 25 Jan 13:51  │           │   ├──  sub-C9ORF364_acq-Philips3T3DT1_desc-conform_T1w.html
.rwxrwxrwx  758k root 25 Jan 15:43  │           │   ├── 󰕙 sub-C9ORF364_acq-Philips3T3DT1_desc-reconall_T1w.svg
.rwxrwxrwx  1.6M root 25 Jan 15:43  │           │   ├── 󰕙 sub-C9ORF364_acq-Philips3T3DT1_dseg.svg
.rwxrwxrwx  799k root 25 Jan 15:43  │           │   ├── 󰕙 sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin6Asym_T1w.svg
.rwxrwxrwx  943k root 25 Jan 15:43  │           │   ├── 󰕙 sub-C9ORF364_acq-Philips3T3DT1_space-MNI152NLin2009cAsym_T1w.svg
.rwxrwxrwx   510 root 25 Jan 13:51  │           │   ├──  sub-C9ORF364_ses-V11_desc-about_T1w.html
.rwxrwxrwx   395 root 25 Jan 13:51  │           │   ├──  sub-C9ORF364_ses-V11_desc-summary_T1w.html
.rwxrwxrwx  186k root 25 Jan 15:43  │           │   ├── 󰕙 sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-carpetplot_bold.svg
.rwxrwxrwx   96k root 25 Jan 15:43  │           │   ├── 󰕙 sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-compcorvar_bold.svg
.rwxrwxrwx  167k root 25 Jan 15:43  │           │   ├── 󰕙 sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-confoundcorr_bold.svg
.rwxrwxrwx  1.1M root 25 Jan 15:43  │           │   ├── 󰕙 sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-coreg_bold.svg
.rwxrwxrwx  519k root 25 Jan 15:43  │           │   ├── 󰕙 sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-rois_bold.svg
.rwxrwxrwx   513 root 25 Jan 14:36  │           │   ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-summary_bold.html
.rwxrwxrwx     0 root 25 Jan 13:51  │           │   ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-validation_bold.html
.rwxrwxrwx  184k root 25 Jan 15:43  │           │   ├── 󰕙 sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-carpetplot_bold.svg
.rwxrwxrwx   96k root 25 Jan 15:43  │           │   ├── 󰕙 sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-compcorvar_bold.svg
.rwxrwxrwx  169k root 25 Jan 15:43  │           │   ├── 󰕙 sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-confoundcorr_bold.svg
.rwxrwxrwx  1.1M root 25 Jan 15:43  │           │   ├── 󰕙 sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-coreg_bold.svg
.rwxrwxrwx  499k root 25 Jan 15:43  │           │   ├── 󰕙 sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-rois_bold.svg
.rwxrwxrwx   513 root 25 Jan 14:36  │           │   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-summary_bold.html
.rwxrwxrwx   269 root 25 Jan 13:51  │           │   └──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-validation_bold.html
drwxrwxrwx     - root 30 Jan 14:46  │           ├──  log
drwxrwxrwx     - root 25 Jan 13:50  │           │   └──  20250125-135022_717e4fbc-8012-4a0f-832c-3d4c312c08af
.rwxrwxrwx  2.2k root 25 Jan 13:50  │           │       └──  fmriprep.toml
drwxrwxrwx     - root 12 Jan 04:41  │           ├──  ses-V11
drwxrwxrwx     - root 25 Jan 14:01  │           │   ├──  anat
.rwxrwxrwx   229 root 25 Jan 14:01  │           │   │   └──  sub-C9ORF364_ses-V11_acq-Philips3T3DT1_from-orig_to-T1w_mode-image_xfm.txt
drwxrwxrwx     - root 25 Jan 15:43  │           │   └──  func
.rwxrwxrwx   120 root 25 Jan 13:58  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-brain_mask.json
.rwxrwxrwx  2.9k root 25 Jan 13:58  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-brain_mask.nii.gz
.rwxrwxrwx   63k root 25 Jan 14:38  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-confounds_timeseries.json
.rwxrwxrwx  454k root 25 Jan 14:38  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-confounds_timeseries.tsv
.rwxrwxrwx   129 root 25 Jan 13:55  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-coreg_boldref.json
.rwxrwxrwx  482k root 25 Jan 13:55  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-coreg_boldref.nii.gz
.rwxrwxrwx   120 root 25 Jan 13:52  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-hmc_boldref.json
.rwxrwxrwx  494k root 25 Jan 13:52  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_desc-hmc_boldref.nii.gz
.rwxrwxrwx   131 root 25 Jan 14:36  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
.rwxrwxrwx   229 root 25 Jan 14:36  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
.rwxrwxrwx   120 root 25 Jan 13:53  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
.rwxrwxrwx   42k root 25 Jan 13:53  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
.rwxrwxrwx   74M root 25 Jan 15:43  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_space-fsLR_den-91k_bold.dtseries.nii
.rwxrwxrwx   713 root 25 Jan 15:43  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_space-fsLR_den-91k_bold.json
.rwxrwxrwx   673 root 25 Jan 15:38  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_space-MNI152NLin6Asym_res-2_boldref.json
.rwxrwxrwx  2.5M root 25 Jan 15:38  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_space-MNI152NLin6Asym_res-2_boldref.nii.gz
.rwxrwxrwx   673 root 25 Jan 15:39  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
.rwxrwxrwx   10k root 25 Jan 15:39  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
.rwxrwxrwx   833 root 25 Jan 15:40  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
.rwxrwxrwx  493M root 25 Jan 15:40  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
.rwxrwxrwx   590 root 25 Jan 15:38  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_space-MNI152NLin2009cAsym_boldref.json
.rwxrwxrwx  528k root 25 Jan 15:38  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_space-MNI152NLin2009cAsym_boldref.nii.gz
.rwxrwxrwx   590 root 25 Jan 15:38  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_space-MNI152NLin2009cAsym_desc-brain_mask.json
.rwxrwxrwx  3.3k root 25 Jan 15:38  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
.rwxrwxrwx   750 root 25 Jan 15:39  │           │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_space-MNI152NLin2009cAsym_desc-preproc_bold.json
.rwxrwxrwx  104M root 25 Jan 15:39  │           │       └──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
drwxrwxrwx     - root 12 Jan 04:41  │           └──  ses-V12
drwxrwxrwx     - root 25 Jan 14:01  │               ├──  anat
.rwxrwxrwx   230 root 25 Jan 14:01  │               │   └──  sub-C9ORF364_ses-V12_acq-Philips3T3DT1_from-orig_to-T1w_mode-image_xfm.txt
drwxrwxrwx     - root 25 Jan 15:43  │               └──  func
.rwxrwxrwx   120 root 25 Jan 13:57  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-brain_mask.json
.rwxrwxrwx  2.9k root 25 Jan 13:57  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-brain_mask.nii.gz
.rwxrwxrwx   72k root 25 Jan 14:38  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-confounds_timeseries.json
.rwxrwxrwx  574k root 25 Jan 14:38  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-confounds_timeseries.tsv
.rwxrwxrwx   129 root 25 Jan 13:54  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-coreg_boldref.json
.rwxrwxrwx  488k root 25 Jan 13:54  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-coreg_boldref.nii.gz
.rwxrwxrwx   120 root 25 Jan 13:52  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-hmc_boldref.json
.rwxrwxrwx  495k root 25 Jan 13:52  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_desc-hmc_boldref.nii.gz
.rwxrwxrwx   131 root 25 Jan 14:36  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
.rwxrwxrwx   232 root 25 Jan 14:36  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
.rwxrwxrwx   120 root 25 Jan 13:53  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
.rwxrwxrwx   42k root 25 Jan 13:53  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
.rwxrwxrwx   74M root 25 Jan 15:43  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_space-fsLR_den-91k_bold.dtseries.nii
.rwxrwxrwx   713 root 25 Jan 15:43  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_space-fsLR_den-91k_bold.json
.rwxrwxrwx   673 root 25 Jan 15:38  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_space-MNI152NLin6Asym_res-2_boldref.json
.rwxrwxrwx  2.6M root 25 Jan 15:38  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_space-MNI152NLin6Asym_res-2_boldref.nii.gz
.rwxrwxrwx   673 root 25 Jan 15:39  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
.rwxrwxrwx   10k root 25 Jan 15:39  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
.rwxrwxrwx   833 root 25 Jan 15:41  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
.rwxrwxrwx  499M root 25 Jan 15:41  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
.rwxrwxrwx   590 root 25 Jan 15:38  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_space-MNI152NLin2009cAsym_boldref.json
.rwxrwxrwx  541k root 25 Jan 15:38  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_space-MNI152NLin2009cAsym_boldref.nii.gz
.rwxrwxrwx   590 root 25 Jan 15:38  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_space-MNI152NLin2009cAsym_desc-brain_mask.json
.rwxrwxrwx  3.1k root 25 Jan 15:38  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
.rwxrwxrwx   750 root 25 Jan 15:40  │                   ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_space-MNI152NLin2009cAsym_desc-preproc_bold.json
.rwxrwxrwx  106M root 25 Jan 15:40  │                   └──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
.rwxrwxrwx    80 root 13 Nov  2024  ├──  participants.json
.rwxrwxrwx   22k root 13 Nov  2024  ├──  participants.tsv
.rwxrwxrwx   612 root 10 Feb 19:25  ├──  README.md
drwxrwxrwx     - root 12 Sep  2024  └──  sub-C9ORF364
drwxrwxrwx     - root 16 Sep  2024      ├──  ses-V11
drwxrwxrwx     - root 12 Sep  2024      │   ├──  anat
.rwxrwxrwx  1.8k root 12 Sep  2024      │   │   ├──  sub-C9ORF364_ses-V11_acq-Philips3T3DT1_T1w.json
.rwxrwxrwx  6.0M root 12 Sep  2024      │   │   ├──  sub-C9ORF364_ses-V11_acq-Philips3T3DT1_T1w.nii.gz
.rwxrwxrwx  1.7k root 12 Sep  2024      │   │   ├──  sub-C9ORF364_ses-V11_acq-Philips3T3DT2_T2w.json
.rwxrwxrwx  5.3M root 12 Sep  2024      │   │   └──  sub-C9ORF364_ses-V11_acq-Philips3T3DT2_T2w.nii.gz
drwxrwxrwx     - root 24 Sep  2024      │   └──  func
.rwxrwxrwx  2.7k root 18 Nov  2024      │       ├──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_bold.json
.rwxrwxrwx   47M root 16 Sep  2024      │       └──  sub-C9ORF364_ses-V11_task-rest_acq-Philips3T_bold.nii.gz
drwxrwxrwx     - root 11 Jan 15:39      └──  ses-V12
drwxrwxrwx     - root 12 Sep  2024          ├──  anat
.rwxrwxrwx  1.8k root 12 Sep  2024          │   ├──  sub-C9ORF364_ses-V12_acq-Philips3T3DT1_T1w.json
.rwxrwxrwx  9.3M root 12 Sep  2024          │   ├──  sub-C9ORF364_ses-V12_acq-Philips3T3DT1_T1w.nii.gz
.rwxrwxrwx  1.7k root 12 Sep  2024          │   ├──  sub-C9ORF364_ses-V12_acq-Philips3T3DT2_T2w.json
.rwxrwxrwx  8.0M root 12 Sep  2024          │   └──  sub-C9ORF364_ses-V12_acq-Philips3T3DT2_T2w.nii.gz
drwxrwxrwx     - root 24 Sep  2024          └──  func
.rwxrwxrwx  2.8k root 18 Nov  2024              ├──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_bold.json
.rwxrwxrwx   47M root 16 Sep  2024              └──  sub-C9ORF364_ses-V12_task-rest_acq-Philips3T_bold.nii.gz

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

#!/bin/bash

# Ensure that TEMPLATEFLOW_HOME is set
if [ -z "$TEMPLATEFLOW_HOME" ]; then
    echo "Error: TEMPLATEFLOW_HOME is not set"
    exit 1
fi
APPTAINERENV_TEMPLATEFLOW_HOME="/templateflow"
APPTAINER_INSTANCE="/home/mpasternak/Applications/apptainer/fmripost-aroma-main.sif"
if [ ! -f "$APPTAINER_INSTANCE" ]; then
    echo "Error: APPTAINER_INSTANCE $APPTAINER_INSTANCE does not exist"
    exit 1
fi

# Case 1: provided a raw BIDS directory as the input
data_dir="/mnt/Samsung_EVO_1TB/AROMA_TEST"
output_dir="$data_dir/derivatives/aroma"
filter_file="/home/mpasternak/Documents/filter.json"

# Ensure the data_dir/derivatives/fmriprep directory exists
if [ ! -d "$data_dir/derivatives/fmriprep" ]; then
    echo "Error: $data_dir/derivatives/fmriprep does not exist"
    exit 1
fi

apptainer run --cleanenv \
    -B $data_dir:/data \
    -B $output_dir:/output \
    -B $TEMPLATEFLOW_HOME:$APPTAINERENV_TEMPLATEFLOW_HOME \
    -B $filter_file:/filters/filter.json \
    $APPTAINER_INSTANCE \
    /data \
    /output \
    participant \
    --derivatives fmriprep=/data/derivatives/fmriprep \
    --participant-label sub-C9ORF364 \
    --bids-filter-file /filters/filter.json \
    --skip-bids-validation \
    --omp-nthreads 8 \
    --random-seed 42 \
    --melodic-dimensionality 68 \
    --aggregate-session-reports 10 \
    -vv

Version:

fMRIPost-AROMA v0.1.dev1+g999b3f5

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

This dataset appears to be BIDS compatible.
        Summary:                  Available Tasks:        Available Modalities: 
        16 Files, 116.37MB        rest                    MRI                   
        1 - Subject                                                             
        2 - Sessions

Relevant log outputs (up to 20 lines):

250210-20:57:18,454 nipype.workflow INFO:
         Raw+derivatives workflow mode enabled
Process Process-2:
Traceback (most recent call last):
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/cli/workflow.py", line 115, in build_workflow
    retval['workflow'] = init_fmripost_aroma_wf()
                         ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/workflows/base.py", line 71, in init_fmripost_aroma_wf
    single_subject_wf = init_single_subject_wf(subject_id)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/workflows/base.py", line 182, in init_single_subject_wf
    subject_data = collect_derivatives(
                   ^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/utils/bids.py", line 232, in collect_derivatives
    item = raw_layout.get(return_type='filename', **query)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/bids/layout/layout.py", line 680, in get
    raise ValueError(msg + "If you're sure you want to impose "
ValueError: 'bold' is not a recognized entity. If you're sure you want to impose this constraint, set invalid_filters='allow'.

tsalo · February 11, 2025, 2:23pm

Could you clarify what you mean by this? fMRIPost-AROMA should primarily work on fMRIPrep derivatives.

I don’t quite understand how this occurred. Part of the problem is that your BIDS filter has “bold” as a key, even though that’s not one of the filter fields for fMRIPost-AROMA, but that doesn’t explain why “bold” is being used as an entity.

Maurice_Pasternak · February 11, 2025, 3:25pm

That if the input directory had been the derivatives fmriprep directory instead of the raw BIDS directory (and therefore the line --derivatives fmriprep=/data/derivatives/fmriprep \ would no longer be necessary either), then the pipeline would fail to gather the derivatives necessary for ICA-AROMA and fail very early on.

I see that I’m not the first to encounter this: Fmripost-aroma error: 'res' or 'desc' is not a recognized entity - #7 by LawsOfForm (“solution 2 worked but not solution 1”)

I can open an issue on GitHub and share a pre-processed single-subject dataset if that helps with both of these issues.

tsalo · February 19, 2025, 2:50pm

@Maurice_Pasternak sorry for the delay.

I don’t think it should fail.

It would be great if you could share your single-subject dataset. I think I could debug this more quickly with access to the data.