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get_s_scan cannot get anatomical scans #120

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grandjeanlab opened this issue Aug 5, 2024 · 0 comments
Open

get_s_scan cannot get anatomical scans #120

grandjeanlab opened this issue Aug 5, 2024 · 0 comments

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@grandjeanlab
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using samri container: https://gin.g-node.org/asmacdo/opfvta-singularity

test data: https://zenodo.org/records/3831124

and following call: apptainer run /project/4180000.41/to_run/opfvta.sing SAMRI generic-prep -m 'DSURQE_100micron_mask.nii.gz' -o . samri_bidsdata-0.3/bids 'DSURQE_100micron_average.nii.gz' > log

I get errors at the get_s_scan node. error reproduded with different datasets, including opfvta_bidsdata-1.0

crashdump :
crashdump.zip

log:
log.txt

relevant error

Traceback (most recent call last):
  File "/usr/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 398, in run
    runtime = self._run_interface(runtime)
  File "/usr/lib/python3.10/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
    out = function_handle(**args)
  File "<string>", line 41, in get_bids_scan
  File "/usr/lib/python3.10/site-packages/pandas/core/base.py", line 347, in item
    raise ValueError("can only convert an array of size 1 to a Python scalar")
ValueError: can only convert an array of size 1 to a Python scalar
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