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Description
Dear CVRmap developers,
We collected some CO2-challenged BOLD images for CVR, and processed them with FMRIPrep with --use-aroma. When trying to run CVRmap, the following error was encountered.
fmriprep_output_dir=${BIDS_dir}/derivatives/fmriprep_${fmriprep_version}
cvrmap_version=2.0.25
singularity run --cleanenv \
-B ${BIDS_dir}:/rawdata \
-B ${BIDS_dir}/derivatives:/derivatives \
-B ${fmriprep_output_dir}:/fmriprep_output \
/path/to/cvrmap.sif \
/rawdata \
/derivatives/cvrmap-${cvrmap_version} \
--participant_label ${subject_ID} \
--skip_bids_validator \
--fmriprep_dir /fmriprep_output \
--task co2 \
participant
INFO (2024-12-03-08-32-56) Version: 2.0.25
INFO (2024-12-03-08-32-56) Indexing BIDS dataset...
INFO (2024-12-03-08-32-58) Defaulting to space MNI152NLin2009cAsym
INFO (2024-12-03-08-32-58) Bids directory: /rawdata
INFO (2024-12-03-08-32-58) Fmriprep directory: /fmriprep_output
INFO (2024-12-03-08-32-58) Subject(s) to analyse: ['vci016']
INFO (2024-12-03-08-32-58) Task to analyse: co2
INFO (2024-12-03-08-32-58) Selected space: MNI152NLin2009cAsym
INFO (2024-12-03-08-32-58) Running for participant vci016
Traceback (most recent call last):
File "/usr/local/bin/cvrmap", line 8, in <module>
sys.exit(main())
^^^^^^
File "/usr/local/lib/python3.11/site-packages/cvrmap/cvrmap.py", line 69, in main
preproc, mni_preproc = get_preproc(basic_filter, layout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/cvrmap/utils/io_tools.py", line 552, in get_preproc
preproc.bids_load(layout, _basic_filter, 'bold')
File "/usr/local/lib/python3.11/site-packages/cvrmap/utils/processing.py", line 59, in bids_load
json_path = layout.get(**filters, extension='json')[0]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range
I wonder if you have any suggestions or insights on this?
Many thanks,
Jiyang
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