fMRIPost-AROMA KeyError: 'session'

scho0011 · July 21, 2025, 5:24am

Hi @tsalo - we are getting the same error as fMRIPost-AROMA error: KeyError: 'session' on certain subs even after updating to the latest container.

Command used

singularity run --cleanenv -B $TEMPLATEFLOW_HOME:/opt/templateflow --home $HOME \
  $container_path \
  $bids_root_dir/fmriprep $bids_root_dir/aroma \
  participant \
  --work-dir $work_dir \
  --derivatives fmriprep=$bids_root_dir/fmriprep \
  --participant-label $subj \
  --skip-bids-validation \
  --denoising-method nonaggr \
  --ignore fieldmaps

Version:

fMRIPost-AROMA 0.1.dev1+g1105d94

Example output from a subjects that errored:

INFO:    gocryptfs not found, will not be able to use gocryptfs
INFO:    underlay of /etc/localtime required more than 50 (100) bind mounts
250721-14:45:31,739 cli WARNING:
	 Telemetry disabled because sentry_sdk is not installed.
/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/cli/workflow.py:42: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import resource_filename as pkgrf
250721-14:48:15,8 nipype.workflow IMPORTANT:
	 Running fMRIPost-AROMA version 0.1.dev1+g1105d94

         License NOTICE ##################################################
         fMRIPost-AROMA 0.1.dev1+g1105d94
         Copyright 2023 The NiPreps Developers.
         
         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).
         
         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.
         
         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.
         
         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
250721-14:49:19,407 nipype.workflow IMPORTANT:
	 Building fMRIPost-AROMA's workflow:
           * BIDS dataset path: /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep.
           * Participant list: ['05S0387'].
           * Run identifier: 20250721-144527_b66fda8b-105d-4732-9f11-02d554943ebc.
           * Output spaces: None.
           * Searching for derivatives: {'fmriprep': PosixPath('/data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep')}.
250721-14:49:19,708 nipype.workflow INFO:
	 Raw+derivatives workflow mode enabled
250721-14:49:19,927 nipype.workflow INFO:
	 Collected subject data:
!!python/object/apply:collections.defaultdict
args:
- !!python/name:builtins.list ''
dictitems:
    bold: &id001
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0387/ses-1/func/sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0387/ses-1/func/sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0387/ses-3/func/sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0387/ses-3/func/sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    bold_raw: *id001

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 280, in init_single_subject_wf
    single_run_wf = init_single_run_wf(bold_file)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/workflows/base.py", line 322, in init_single_run_wf
    collect_derivatives(
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/utils/bids.py", line 143, in collect_derivatives
    item_sessions = [layout.get_file(f).entities['session'] for f in item]
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/utils/bids.py", line 143, in <listcomp>
    item_sessions = [layout.get_file(f).entities['session'] for f in item]
                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/sqlalchemy/ext/associationproxy.py", line 1662, in __getitem__
    return self._get(self.col[key])
                     ~~~~~~~~^^^^^
KeyError: 'session'

fmriprep file tree for the above subject:

.
├── anat
│   ├── sub-05S0387_acq-spc2_run-3_desc-preproc_T2w.json
│   ├── sub-05S0387_acq-spc2_run-3_desc-preproc_T2w.nii.gz
│   ├── sub-05S0387_acq-tfl3_run-2_desc-brain_mask.json
│   ├── sub-05S0387_acq-tfl3_run-2_desc-brain_mask.nii.gz
│   ├── sub-05S0387_acq-tfl3_run-2_desc-preproc_T1w.json
│   ├── sub-05S0387_acq-tfl3_run-2_desc-preproc_T1w.nii.gz
│   ├── sub-05S0387_acq-tfl3_run-2_desc-ribbon_mask.json
│   ├── sub-05S0387_acq-tfl3_run-2_desc-ribbon_mask.nii.gz
│   ├── sub-05S0387_acq-tfl3_run-2_dseg.nii.gz
│   ├── sub-05S0387_acq-tfl3_run-2_from-fsnative_to-T1w_mode-image_xfm.txt
│   ├── sub-05S0387_acq-tfl3_run-2_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
│   ├── sub-05S0387_acq-tfl3_run-2_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
│   ├── sub-05S0387_acq-tfl3_run-2_from-T1w_to-fsnative_mode-image_xfm.txt
│   ├── sub-05S0387_acq-tfl3_run-2_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
│   ├── sub-05S0387_acq-tfl3_run-2_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-L_midthickness.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-L_pial.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-L_space-fsaverage_desc-reg_sphere.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-L_space-fsLR_den-32k_midthickness.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-L_space-fsLR_den-32k_pial.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-L_space-fsLR_den-32k_white.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-L_sphere.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-L_sulc.shape.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-L_thickness.shape.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-L_white.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-R_midthickness.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-R_pial.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-R_space-fsLR_den-32k_midthickness.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-R_space-fsLR_den-32k_pial.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-R_space-fsLR_den-32k_white.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-R_sphere.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-R_sulc.shape.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-R_thickness.shape.gii
│   ├── sub-05S0387_acq-tfl3_run-2_hemi-R_white.surf.gii
│   ├── sub-05S0387_acq-tfl3_run-2_label-CSF_probseg.nii.gz
│   ├── sub-05S0387_acq-tfl3_run-2_label-GM_probseg.nii.gz
│   ├── sub-05S0387_acq-tfl3_run-2_label-WM_probseg.nii.gz
│   ├── sub-05S0387_acq-tfl3_run-2_space-fsLR_den-91k_curv.dscalar.nii
│   ├── sub-05S0387_acq-tfl3_run-2_space-fsLR_den-91k_curv.json
│   ├── sub-05S0387_acq-tfl3_run-2_space-fsLR_den-91k_sulc.dscalar.nii
│   ├── sub-05S0387_acq-tfl3_run-2_space-fsLR_den-91k_sulc.json
│   ├── sub-05S0387_acq-tfl3_run-2_space-fsLR_den-91k_thickness.dscalar.nii
│   ├── sub-05S0387_acq-tfl3_run-2_space-fsLR_den-91k_thickness.json
│   ├── sub-05S0387_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│   ├── sub-05S0387_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│   ├── sub-05S0387_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.json
│   ├── sub-05S0387_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
│   ├── sub-05S0387_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_dseg.json
│   ├── sub-05S0387_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_dseg.nii.gz
│   ├── sub-05S0387_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_label-CSF_probseg.nii.gz
│   ├── sub-05S0387_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_label-GM_probseg.nii.gz
│   └── sub-05S0387_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_label-WM_probseg.nii.gz
├── figures
│   ├── sub-05S0387_acq-tfl3_run-2_desc-conform_T1w.html
│   ├── sub-05S0387_acq-tfl3_run-2_desc-reconall_T1w.svg
│   ├── sub-05S0387_acq-tfl3_run-2_dseg.svg
│   ├── sub-05S0387_acq-tfl3_run-2_space-MNI152NLin6Asym_T1w.svg
│   ├── sub-05S0387_ses-1_acq-tfl3_run-2_desc-conform_T1w.html
│   ├── sub-05S0387_ses-1_acq-tfl3_run-2_desc-reconall_T1w.svg
│   ├── sub-05S0387_ses-1_acq-tfl3_run-2_dseg.svg
│   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-MNI152NLin6Asym_T1w.svg
│   ├── sub-05S0387_ses-1_desc-about_T1w.html
│   ├── sub-05S0387_ses-1_desc-summary_T1w.html
│   ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-carpetplot_bold.svg
│   ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-compcorvar_bold.svg
│   ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-confoundcorr_bold.svg
│   ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_bold.svg
│   ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-rois_bold.svg
│   ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-summary_bold.html
│   ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-validation_bold.html
│   ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-carpetplot_bold.svg
│   ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-compcorvar_bold.svg
│   ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confoundcorr_bold.svg
│   ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-coreg_bold.svg
│   ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-rois_bold.svg
│   ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-summary_bold.html
│   ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-validation_bold.html
│   ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-carpetplot_bold.svg
│   ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-compcorvar_bold.svg
│   ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-confoundcorr_bold.svg
│   ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_bold.svg
│   ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-rois_bold.svg
│   ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-summary_bold.html
│   ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-validation_bold.html
│   ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-carpetplot_bold.svg
│   ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-compcorvar_bold.svg
│   ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confoundcorr_bold.svg
│   ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-coreg_bold.svg
│   ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-rois_bold.svg
│   ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-summary_bold.html
│   └── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-validation_bold.html
├── log
│   ├── 20250707-112021_f5ed56f1-4bb1-4df8-b3b1-61f9e3362dbc
│   │   └── fmriprep.toml
│   └── 20250710-130600_6f500cb9-7df9-409a-a482-ae08f9848d8f
│       └── fmriprep.toml
├── ses-1
│   ├── anat
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_desc-brain_mask.json
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_desc-brain_mask.nii.gz
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_desc-preproc_T1w.json
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_desc-preproc_T1w.nii.gz
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_desc-ribbon_mask.json
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_desc-ribbon_mask.nii.gz
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_dseg.nii.gz
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_from-fsnative_to-T1w_mode-image_xfm.txt
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_from-orig_to-T1w_mode-image_xfm.txt
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_from-T1w_to-fsnative_mode-image_xfm.txt
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-L_midthickness.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-L_pial.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-L_space-fsaverage_desc-reg_sphere.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-L_space-fsLR_den-32k_midthickness.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-L_space-fsLR_den-32k_pial.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-L_space-fsLR_den-32k_white.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-L_sphere.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-L_sulc.shape.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-L_thickness.shape.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-L_white.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-R_midthickness.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-R_pial.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-R_space-fsLR_den-32k_midthickness.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-R_space-fsLR_den-32k_pial.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-R_space-fsLR_den-32k_white.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-R_sphere.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-R_sulc.shape.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-R_thickness.shape.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_hemi-R_white.surf.gii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_label-CSF_probseg.nii.gz
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_label-GM_probseg.nii.gz
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_label-WM_probseg.nii.gz
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-fsLR_den-91k_curv.dscalar.nii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-fsLR_den-91k_curv.json
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-fsLR_den-91k_sulc.dscalar.nii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-fsLR_den-91k_sulc.json
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-fsLR_den-91k_thickness.dscalar.nii
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-fsLR_den-91k_thickness.json
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.json
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_dseg.json
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_dseg.nii.gz
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_label-CSF_probseg.nii.gz
│   │   ├── sub-05S0387_ses-1_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_label-GM_probseg.nii.gz
│   │   └── sub-05S0387_ses-1_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_label-WM_probseg.nii.gz
│   └── func
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.nii.gz
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.tsv
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_boldref.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_boldref.nii.gz
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-hmc_boldref.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-hmc_boldref.nii.gz
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_space-fsLR_den-91k_bold.dtseries.nii
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_space-fsLR_den-91k_bold.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_boldref.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_boldref.nii.gz
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-brain_mask.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-brain_mask.nii.gz
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confounds_timeseries.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confounds_timeseries.tsv
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-coreg_boldref.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-coreg_boldref.nii.gz
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-hmc_boldref.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-hmc_boldref.nii.gz
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_space-fsLR_den-91k_bold.dtseries.nii
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_space-fsLR_den-91k_bold.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_boldref.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_boldref.nii.gz
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│       ├── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
│       └── sub-05S0387_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
└── ses-3
    ├── anat
    │   └── sub-05S0387_ses-3_acq-tfl3_run-2_from-orig_to-T1w_mode-image_xfm.txt
    └── func
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.nii.gz
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.tsv
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_boldref.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_boldref.nii.gz
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-hmc_boldref.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-hmc_boldref.nii.gz
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-fsLR_den-91k_bold.dtseries.nii
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-fsLR_den-91k_bold.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_boldref.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_boldref.nii.gz
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-brain_mask.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-brain_mask.nii.gz
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confounds_timeseries.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confounds_timeseries.tsv
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-coreg_boldref.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-coreg_boldref.nii.gz
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-hmc_boldref.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-hmc_boldref.nii.gz
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_space-fsLR_den-91k_bold.dtseries.nii
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_space-fsLR_den-91k_bold.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_boldref.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_boldref.nii.gz
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
        ├── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
        └── sub-05S0387_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz

Please let me know if you needed any more info. Thanks for you help on this and for making the container!

scho0011 · July 21, 2025, 5:28am

@tsalo incase it helps with the above here is info on a subject from same dataset where the container worked fine. Note that I had to remove the ses-6 from the fmriprep file list output to meet char limits.

Example first 20 lines from a subject that did not error:

INFO:    gocryptfs not found, will not be able to use gocryptfs
INFO:    underlay of /etc/localtime required more than 50 (100) bind mounts
250721-14:54:01,226 cli WARNING:
	 Telemetry disabled because sentry_sdk is not installed.
/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/cli/workflow.py:42: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import resource_filename as pkgrf
250721-14:56:45,617 nipype.workflow IMPORTANT:
	 Running fMRIPost-AROMA version 0.1.dev1+g1105d94

         License NOTICE ##################################################
         fMRIPost-AROMA 0.1.dev1+g1105d94
         Copyright 2023 The NiPreps Developers.
         
         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).
         
         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.
         
         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.
         
         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
250721-14:57:49,640 nipype.workflow IMPORTANT:
	 Building fMRIPost-AROMA's workflow:
           * BIDS dataset path: /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep.
           * Participant list: ['05S0351'].
           * Run identifier: 20250721-145357_d7f65146-7f13-4101-892e-0ae0b8fbfb66.
           * Output spaces: None.
           * Searching for derivatives: {'fmriprep': PosixPath('/data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep')}.
250721-14:57:49,914 nipype.workflow INFO:
	 Raw+derivatives workflow mode enabled
250721-14:57:50,134 nipype.workflow INFO:
	 Collected subject data:
!!python/object/apply:collections.defaultdict
args:
- !!python/name:builtins.list ''
dictitems:
    bold: &id001
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/ses-2/func/sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/ses-2/func/sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/ses-3/func/sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/ses-3/func/sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/ses-4/func/sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/ses-4/func/sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/ses-6/func/sub-05S0351_ses-6_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/ses-6/func/sub-05S0351_ses-6_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    bold_raw: *id001

250721-15:00:07,3 nipype.workflow INFO:
	 Collected run data for sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz:
!!python/object/apply:collections.defaultdict
args:
- !!python/name:builtins.list ''
dictitems:
    anat2mni152nlin6asym: /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/anat/sub-05S0351_acq-tfl3_run-2_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
    anat2outputspaces_xfm:
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/anat/sub-05S0351_acq-tfl3_run-2_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
    anat_dseg: /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/anat/sub-05S0351_acq-tfl3_run-2_dseg.nii.gz
    anat_mni152nlin6asym: /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/anat/sub-05S0351_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
    bold_confounds: /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/ses-2/func/sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.tsv
    bold_mask_mni152nlin6asym: /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/ses-2/func/sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
    bold_mask_outputspaces:
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/ses-2/func/sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
    bold_mni152nlin6asym: /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/ses-2/func/sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    bold_outputspaces:
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/ses-2/func/sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    bold_raw: /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0351/ses-2/func/sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz

[...]

fmriprep file tree for the above subject that did not error:

.
├── anat
│   ├── sub-05S0351_acq-spc2_run-3_desc-preproc_T2w.json
│   ├── sub-05S0351_acq-spc2_run-3_desc-preproc_T2w.nii.gz
│   ├── sub-05S0351_acq-tfl3_run-2_desc-brain_mask.json
│   ├── sub-05S0351_acq-tfl3_run-2_desc-brain_mask.nii.gz
│   ├── sub-05S0351_acq-tfl3_run-2_desc-preproc_T1w.json
│   ├── sub-05S0351_acq-tfl3_run-2_desc-preproc_T1w.nii.gz
│   ├── sub-05S0351_acq-tfl3_run-2_desc-ribbon_mask.json
│   ├── sub-05S0351_acq-tfl3_run-2_desc-ribbon_mask.nii.gz
│   ├── sub-05S0351_acq-tfl3_run-2_dseg.nii.gz
│   ├── sub-05S0351_acq-tfl3_run-2_from-fsnative_to-T1w_mode-image_xfm.txt
│   ├── sub-05S0351_acq-tfl3_run-2_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
│   ├── sub-05S0351_acq-tfl3_run-2_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
│   ├── sub-05S0351_acq-tfl3_run-2_from-T1w_to-fsnative_mode-image_xfm.txt
│   ├── sub-05S0351_acq-tfl3_run-2_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
│   ├── sub-05S0351_acq-tfl3_run-2_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-L_midthickness.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-L_pial.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-L_space-fsaverage_desc-reg_sphere.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-L_space-fsLR_den-32k_midthickness.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-L_space-fsLR_den-32k_pial.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-L_space-fsLR_den-32k_white.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-L_sphere.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-L_sulc.shape.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-L_thickness.shape.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-L_white.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-R_midthickness.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-R_pial.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-R_space-fsLR_den-32k_midthickness.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-R_space-fsLR_den-32k_pial.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-R_space-fsLR_den-32k_white.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-R_sphere.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-R_sulc.shape.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-R_thickness.shape.gii
│   ├── sub-05S0351_acq-tfl3_run-2_hemi-R_white.surf.gii
│   ├── sub-05S0351_acq-tfl3_run-2_label-CSF_probseg.nii.gz
│   ├── sub-05S0351_acq-tfl3_run-2_label-GM_probseg.nii.gz
│   ├── sub-05S0351_acq-tfl3_run-2_label-WM_probseg.nii.gz
│   ├── sub-05S0351_acq-tfl3_run-2_space-fsLR_den-91k_curv.dscalar.nii
│   ├── sub-05S0351_acq-tfl3_run-2_space-fsLR_den-91k_curv.json
│   ├── sub-05S0351_acq-tfl3_run-2_space-fsLR_den-91k_sulc.dscalar.nii
│   ├── sub-05S0351_acq-tfl3_run-2_space-fsLR_den-91k_sulc.json
│   ├── sub-05S0351_acq-tfl3_run-2_space-fsLR_den-91k_thickness.dscalar.nii
│   ├── sub-05S0351_acq-tfl3_run-2_space-fsLR_den-91k_thickness.json
│   ├── sub-05S0351_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│   ├── sub-05S0351_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│   ├── sub-05S0351_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.json
│   ├── sub-05S0351_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
│   ├── sub-05S0351_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_dseg.json
│   ├── sub-05S0351_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_dseg.nii.gz
│   ├── sub-05S0351_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_label-CSF_probseg.nii.gz
│   ├── sub-05S0351_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_label-GM_probseg.nii.gz
│   └── sub-05S0351_acq-tfl3_run-2_space-MNI152NLin6Asym_res-2_label-WM_probseg.nii.gz
├── figures
│   ├── sub-05S0351_acq-tfl3_run-2_desc-conform_T1w.html
│   ├── sub-05S0351_acq-tfl3_run-2_desc-reconall_T1w.svg
│   ├── sub-05S0351_acq-tfl3_run-2_dseg.svg
│   ├── sub-05S0351_acq-tfl3_run-2_space-MNI152NLin6Asym_T1w.svg
│   ├── sub-05S0351_ses-2_desc-about_T1w.html
│   ├── sub-05S0351_ses-2_desc-summary_T1w.html
│   ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-carpetplot_bold.svg
│   ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-compcorvar_bold.svg
│   ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-confoundcorr_bold.svg
│   ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_bold.svg
│   ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-rois_bold.svg
│   ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-summary_bold.html
│   ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-validation_bold.html
│   ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-carpetplot_bold.svg
│   ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-compcorvar_bold.svg
│   ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confoundcorr_bold.svg
│   ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-coreg_bold.svg
│   ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-rois_bold.svg
│   ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-summary_bold.html
│   ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-validation_bold.html
│   ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-carpetplot_bold.svg
│   ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-compcorvar_bold.svg
│   ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-confoundcorr_bold.svg
│   ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_bold.svg
│   ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-rois_bold.svg
│   ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-summary_bold.html
│   ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-validation_bold.html
│   ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-carpetplot_bold.svg
│   ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-compcorvar_bold.svg
│   ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-confoundcorr_bold.svg
│   ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-coreg_bold.svg
│   ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-rois_bold.svg
│   ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-summary_bold.html
│   ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-validation_bold.html
│   ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-carpetplot_bold.svg
│   ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-compcorvar_bold.svg
│   ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-confoundcorr_bold.svg
│   ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_bold.svg
│   ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-rois_bold.svg
│   ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-summary_bold.html
│   ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-validation_bold.html
│   ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-carpetplot_bold.svg
│   ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-compcorvar_bold.svg
│   ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confoundcorr_bold.svg
│   ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-coreg_bold.svg
│   ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-rois_bold.svg
│   ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-summary_bold.html
│   ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-validation_bold.html
│   ├── sub-05S0351_ses-6_task-rest_acq-epfid2_dir-AP_run-8_desc-carpetplot_bold.svg
│   ├── sub-05S0351_ses-6_task-rest_acq-epfid2_dir-AP_run-8_desc-compcorvar_bold.svg
│   ├── sub-05S0351_ses-6_task-rest_acq-epfid2_dir-AP_run-8_desc-confoundcorr_bold.svg
│   ├── sub-05S0351_ses-6_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_bold.svg
│   ├── sub-05S0351_ses-6_task-rest_acq-epfid2_dir-AP_run-8_desc-rois_bold.svg
│   ├── sub-05S0351_ses-6_task-rest_acq-epfid2_dir-AP_run-8_desc-summary_bold.html
│   ├── sub-05S0351_ses-6_task-rest_acq-epfid2_dir-AP_run-8_desc-validation_bold.html
│   ├── sub-05S0351_ses-6_task-rest_acq-epfid2m5_dir-AP_run-11_desc-carpetplot_bold.svg
│   ├── sub-05S0351_ses-6_task-rest_acq-epfid2m5_dir-AP_run-11_desc-compcorvar_bold.svg
│   ├── sub-05S0351_ses-6_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confoundcorr_bold.svg
│   ├── sub-05S0351_ses-6_task-rest_acq-epfid2m5_dir-AP_run-11_desc-coreg_bold.svg
│   ├── sub-05S0351_ses-6_task-rest_acq-epfid2m5_dir-AP_run-11_desc-rois_bold.svg
│   ├── sub-05S0351_ses-6_task-rest_acq-epfid2m5_dir-AP_run-11_desc-summary_bold.html
│   └── sub-05S0351_ses-6_task-rest_acq-epfid2m5_dir-AP_run-11_desc-validation_bold.html
├── log
│   ├── 20250710-125319_3bd2e278-a4d2-4d50-bb5e-458fc5501a6a
│   │   └── fmriprep.toml
│   └── 20250711-161736_195b1d49-49d6-4486-aaf6-274e52b7de39
│       └── fmriprep.toml
├── ses-2
│   ├── anat
│   │   └── sub-05S0351_ses-2_acq-tfl3_run-2_from-orig_to-T1w_mode-image_xfm.txt
│   └── func
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.nii.gz
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.tsv
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_boldref.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_boldref.nii.gz
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-hmc_boldref.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_desc-hmc_boldref.nii.gz
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-fsLR_den-91k_bold.dtseries.nii
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-fsLR_den-91k_bold.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_boldref.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_boldref.nii.gz
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-brain_mask.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-brain_mask.nii.gz
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confounds_timeseries.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confounds_timeseries.tsv
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-coreg_boldref.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-coreg_boldref.nii.gz
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-hmc_boldref.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_desc-hmc_boldref.nii.gz
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_space-fsLR_den-91k_bold.dtseries.nii
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_space-fsLR_den-91k_bold.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_boldref.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_boldref.nii.gz
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│       ├── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
│       └── sub-05S0351_ses-2_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
├── ses-3
│   ├── anat
│   │   └── sub-05S0351_ses-3_acq-tfl3_run-2_from-orig_to-T1w_mode-image_xfm.txt
│   └── func
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.nii.gz
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.tsv
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_boldref.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_boldref.nii.gz
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-hmc_boldref.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-hmc_boldref.nii.gz
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-fsLR_den-91k_bold.dtseries.nii
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-fsLR_den-91k_bold.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_boldref.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_boldref.nii.gz
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-brain_mask.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-brain_mask.nii.gz
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-confounds_timeseries.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-confounds_timeseries.tsv
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-coreg_boldref.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-coreg_boldref.nii.gz
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-hmc_boldref.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_desc-hmc_boldref.nii.gz
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_space-fsLR_den-91k_bold.dtseries.nii
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_space-fsLR_den-91k_bold.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_space-MNI152NLin6Asym_res-2_boldref.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_space-MNI152NLin6Asym_res-2_boldref.nii.gz
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│       ├── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
│       └── sub-05S0351_ses-3_task-rest_acq-epfid2m5_dir-AP_run-12_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
├── ses-4
│   ├── anat
│   │   └── sub-05S0351_ses-4_acq-tfl3_run-2_from-orig_to-T1w_mode-image_xfm.txt
│   └── func
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.nii.gz
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.tsv
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_boldref.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-coreg_boldref.nii.gz
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-hmc_boldref.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_desc-hmc_boldref.nii.gz
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_space-fsLR_den-91k_bold.dtseries.nii
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_space-fsLR_den-91k_bold.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_boldref.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_boldref.nii.gz
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-brain_mask.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-brain_mask.nii.gz
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confounds_timeseries.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confounds_timeseries.tsv
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-coreg_boldref.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-coreg_boldref.nii.gz
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-hmc_boldref.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_desc-hmc_boldref.nii.gz
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_space-fsLR_den-91k_bold.dtseries.nii
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_space-fsLR_den-91k_bold.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_boldref.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_boldref.nii.gz
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│       ├── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
│       └── sub-05S0351_ses-4_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz

tsalo · July 22, 2025, 12:47pm

It looks like you passed the fMRIPrep derivatives in as both the input dataset (fmripost_aroma <in_dir> <out_dir>) and as a separate dataset via the --derivatives flag, and the fMRIPrep derivatives are being indexed twice as a result.

Please try either passing in the raw BIDS dataset as the input dataset or dropping the --derivatives flag (not both).

Evangeline · July 23, 2025, 4:59am

Hi @tsalo , I’m working with @scho0011 on this error. I tried dropping the --derivative flag but still got the same error:

250723-12:19:51,764 cli WARNING:
	 Telemetry disabled because sentry_sdk is not installed.
/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/cli/workflow.py:42: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import resource_filename as pkgrf
250723-12:23:02,320 nipype.workflow IMPORTANT:
	 Running fMRIPost-AROMA version 0.1.dev1+g1105d94

         License NOTICE ##################################################
         fMRIPost-AROMA 0.1.dev1+g1105d94
         Copyright 2023 The NiPreps Developers.
         
         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).
         
         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.
         
         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.
         
         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
250723-12:24:04,422 nipype.workflow IMPORTANT:
	 Building fMRIPost-AROMA's workflow:
           * BIDS dataset path: /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep.
           * Participant list: ['05S0352'].
           * Run identifier: 20250723-121946_a2c14221-eebd-4047-b005-df60d5562eff.
           * Output spaces: None.
250723-12:24:04,783 nipype.workflow INFO:
	 Derivatives-only workflow mode enabled
250723-12:24:06,339 nipype.workflow INFO:
	 Collected subject data:
!!python/object/apply:collections.defaultdict
args:
- !!python/name:builtins.list ''
dictitems:
    anat2mni152nlin6asym: /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/anat/sub-05S0352_acq-tfl3_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
    anat_dseg: /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/anat/sub-05S0352_acq-tfl3_dseg.nii.gz
    anat_mni152nlin6asym: /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/anat/sub-05S0352_acq-tfl3_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
    bold: &id001
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-1/func/sub-05S0352_ses-1_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-1/func/sub-05S0352_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-3/func/sub-05S0352_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-3/func/sub-05S0352_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-5/func/sub-05S0352_ses-5_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-5/func/sub-05S0352_ses-5_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-7/func/sub-05S0352_ses-7_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-7/func/sub-05S0352_ses-7_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-8/func/sub-05S0352_ses-8_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
    bold_confounds:
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-1/func/sub-05S0352_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.tsv
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-1/func/sub-05S0352_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confounds_timeseries.tsv
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-3/func/sub-05S0352_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.tsv
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-3/func/sub-05S0352_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confounds_timeseries.tsv
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-5/func/sub-05S0352_ses-5_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.tsv
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-5/func/sub-05S0352_ses-5_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confounds_timeseries.tsv
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-7/func/sub-05S0352_ses-7_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.tsv
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-7/func/sub-05S0352_ses-7_task-rest_acq-epfid2m5_dir-AP_run-11_desc-confounds_timeseries.tsv
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-8/func/sub-05S0352_ses-8_task-rest_acq-epfid2_dir-AP_run-8_desc-confounds_timeseries.tsv
    bold_hmc:
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-1/func/sub-05S0352_ses-1_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-1/func/sub-05S0352_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-3/func/sub-05S0352_ses-3_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-3/func/sub-05S0352_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-5/func/sub-05S0352_ses-5_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-5/func/sub-05S0352_ses-5_task-rest_acq-epfid2m5_dir-AP_run-11_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-7/func/sub-05S0352_ses-7_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-7/func/sub-05S0352_ses-7_task-rest_acq-epfid2m5_dir-AP_run-11_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-8/func/sub-05S0352_ses-8_task-rest_acq-epfid2_dir-AP_run-8_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
    bold_mask_mni152nlin6asym:
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-1/func/sub-05S0352_ses-1_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-1/func/sub-05S0352_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-3/func/sub-05S0352_ses-3_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-3/func/sub-05S0352_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-5/func/sub-05S0352_ses-5_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-5/func/sub-05S0352_ses-5_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-7/func/sub-05S0352_ses-7_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-7/func/sub-05S0352_ses-7_task-rest_acq-epfid2m5_dir-AP_run-11_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-8/func/sub-05S0352_ses-8_task-rest_acq-epfid2_dir-AP_run-8_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
    bold_mask_native:
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-1/func/sub-05S0352_ses-1_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-1/func/sub-05S0352_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-3/func/sub-05S0352_ses-3_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-3/func/sub-05S0352_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-5/func/sub-05S0352_ses-5_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-5/func/sub-05S0352_ses-5_task-rest_acq-epfid2m5_dir-AP_run-11_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-7/func/sub-05S0352_ses-7_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-7/func/sub-05S0352_ses-7_task-rest_acq-epfid2m5_dir-AP_run-11_desc-brain_mask.nii.gz
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-8/func/sub-05S0352_ses-8_task-rest_acq-epfid2_dir-AP_run-8_desc-brain_mask.nii.gz
    bold_mni152nlin6asym: *id001
    boldref2anat:
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-1/func/sub-05S0352_ses-1_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-1/func/sub-05S0352_ses-1_task-rest_acq-epfid2m5_dir-AP_run-11_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-3/func/sub-05S0352_ses-3_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-3/func/sub-05S0352_ses-3_task-rest_acq-epfid2m5_dir-AP_run-11_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-5/func/sub-05S0352_ses-5_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-5/func/sub-05S0352_ses-5_task-rest_acq-epfid2m5_dir-AP_run-11_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-7/func/sub-05S0352_ses-7_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-7/func/sub-05S0352_ses-7_task-rest_acq-epfid2m5_dir-AP_run-11_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
    - /data/projects/punim2529/NAPLS/Raw_data/derivatives/fmriprep/sub-05S0352/ses-8/func/sub-05S0352_ses-8_task-rest_acq-epfid2_dir-AP_run-8_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
    boldref2fmap: null

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 280, in init_single_subject_wf
    single_run_wf = init_single_run_wf(bold_file)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/workflows/base.py", line 347, in init_single_run_wf
    collect_derivatives(
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/utils/bids.py", line 143, in collect_derivatives
    item_sessions = [layout.get_file(f).entities['session'] for f in item]
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/fmripost_aroma/utils/bids.py", line 143, in <listcomp>
    item_sessions = [layout.get_file(f).entities['session'] for f in item]
                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
  File "/opt/conda/envs/fmripost_aroma/lib/python3.11/site-packages/sqlalchemy/ext/associationproxy.py", line 1662, in __getitem__
    return self._get(self.col[key])
                     ~~~~~~~~^^^^^
KeyError: 'session'

Do you have any idea on what might cause the error? Thank you so much for your help!

tsalo · July 23, 2025, 1:52pm

I’m taking a look now. Why do you have session-wise preprocessed anatomical files and ones at the subject level? I don’t believe that’s something that fMRIPrep supports.