Summary of what happened:
I am attempting to use fmripost-aroma but am encountering difficulties with some of the specifications that I previously had not encountered when ICA-AROMA was still integrated in fmriprep. I have gotten various errors (related to dummy scans, extraction of motion parameters, etc.), which leads me to think that my initial specification within the command is incorrect/incomple. I did not yet find a clear documentation for troubleshooting with fmripost-aroma. I based my specification based on this post but know it may differ.
Any ideas what aspects of the command may be incorrect or where to look (beyond the relatively limited fmripost-aroma read the docs)?
Command used (and if a helper script was used, a link to the helper script or the command generated):
fmriprep:
fmriprep-docker {$PROJ_DIR}/niftidata/ {$PROJ_DIR}/2_fmriprep participant --participant-label P001 --fs-license-file {$PROJ_DIR}/FreeSurfer/license.txt --bids-filter-file {$PROJ_DIR}/2_fmriprep/code/P001_for-bids-filter-file.json --output-spaces MNI152NLin6Asym:res-02 --nthreads 24 --omp-nthreads 8
fmripost-aroma
docker run --rm -it \
-v {$PROJ_DIR}/niftidata:/data \
-v {$PROJ_DIR}/3_fmripost-aroma:/out \
-v {$PROJ_DIR}/2_fmriprep:/prep \
nipreps/fmripost-aroma:main \
/data \
/out \
participant \
--derivatives fmriprep=/prep \
--denoising-method nonaggr \
--participant-label P001
Version:
Presumably the latest version as pulled from here: GitHub - nipreps/fmripost-aroma: Run ICA-AROMA on fMRIPrep derivatives · GitHub .
I cannot get the fmripost-aroma -h to work to check the version.
Environment (Docker, Singularity / Apptainer, custom installation):
Both fmriprep and fmripost-aroma were installed with Docker containerization.
Data formatted according to a validatable standard? Please provide the output of the validator:
The data was already run through fmriprep without issues (–skip-bids-validation was not set).
Relevant log outputs (up to 20 lines):
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 334, in init_single_run_wf
raise ValueError(
ValueError: No confounds detected. Automatical dummy scan detection cannot be performed. Please set the `--dummy-scans` flag explicitly.
Edit: I did already insert --dummy-scans with some value. However, this lent to subsequent issues, such as the extraction of motion parameters mentioned in the summary. This made me think that my initial command was anyways incorrect and the source of the issue that I am unsure how to solve.