Summary of what happened:
First-time user. I ran fMRIPost-AROMA on docker. Spits an error message “No BOLD images found.”
Command used (and if a helper script was used, a link to the helper script or the command generated):
docker run --rm -it \
-v ~/mridata/pilot_aaf/derivatives/fmriprep:/prep:ro \
-v ~/mridata/pilot_aaf/derivatives/fmripost_aroma:/out \
-v ~/mridata/pilot_aaf/work/fmripost_aroma:/work \
nipreps/fmripost-aroma:main \
/prep /out participant \
--skip_bids_validation \
--participant-label 03 \
--denoising-method aggr \
--melodic-dimensionality 20 \
--nprocs 8 \
--omp-nthreads 2 \
--mem 24000 \
--error-on-warnings \
--notrack \
-w /work
Version:
fMRIPost-AROMA version 0.1.dev1+g965d73c
fmriprep 24.0.1
Environment (Docker, Singularity / Apptainer, custom installation):
Ubuntu 20.04.6 LTS, Docker 4.33.0
Data formatted according to a validatable standard? Please provide the output of the validator:
Relevant log outputs (up to 20 lines):
250314-00:39:28,333 nipype.workflow IMPORTANT:
Building fMRIPost-AROMA's workflow:
* BIDS dataset path: /prep.
* Participant list: ['03'].
* Run identifier: 20250314-003914_5412ef98-c56b-4ae3-9aae-17af47170915.
* Output spaces: None.
250314-00:39:28,965 nipype.workflow INFO:
Derivatives-only 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 208, in init_single_subject_wf
raise RuntimeError(
RuntimeError: No BOLD images found for participant 03 and task <all>. All workflows require BOLD images. Please check your BIDS filters: None.
Screenshots / relevant information:
I am new to fMRI data analysis. The trial in my experimental paradigm involves some movement, making motion correction essential. That’s why I am trying to use ICA-AROMA and came across this software. However, I am having trouble running it, as it fails to recognize the BOLD images.
I have triple-checked that the subject directory, the func sub-directory, and all relevant BOLD images are correctly organized, but the issue persists.
~/mridata/pilot_aaf/derivatives/fmriprep/sub-03/func$ ls
...
sub-03_task-aaf_run-01_desc-brain_mask.json
sub-03_task-aaf_run-01_desc-brain_mask.nii.gz
sub-03_task-aaf_run-01_desc-confounds_timeseries.json
sub-03_task-aaf_run-01_desc-confounds_timeseries.tsv
sub-03_task-aaf_run-01_desc-coreg_boldref.json
sub-03_task-aaf_run-01_desc-coreg_boldref.nii.gz
sub-03_task-aaf_run-01_desc-hmc_boldref.json
sub-03_task-aaf_run-01_desc-hmc_boldref.nii.gz
sub-03_task-aaf_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-03_task-aaf_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-03_task-aaf_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
sub-03_task-aaf_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
sub-03_task-aaf_run-01_space-MNI152NLin2009cAsym_res-2_boldref.json
sub-03_task-aaf_run-01_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
sub-03_task-aaf_run-01_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
sub-03_task-aaf_run-01_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
sub-03_task-aaf_run-01_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json
sub-03_task-aaf_run-01_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz
Thank you in advance.
