Closed laurelrr closed 11 months ago
@laurelrr In the single session conversion script (neurotensin_valence_convert_session.py
) you would provide the metadata for the subject in subject_metadata
, just how you did as
subject_metadata = dict(sex="M",age="P60D",genotype="Wild type",strain="C57BL/6J")
But subject_id
is a required property that you don't have in subject_metadata which could be provided as:
subject_metadata = dict(subject_id="H01", sex="M",age="P60D",genotype="Wild type",strain="C57BL/6J")
Now the pipeline could automatically determine subject_id from the confocal images file name (e.g. H41PVT_40x.oif would be H41), but if you're not using that interface then it should be provided manually by providing it in the subject_metadata
dict.
If you are using the parallel conversion script (neurotensin_valence_convert_all_sessions.py
) the subject_id
is extracted from the column with the name "subject_id" for each session that you want to convert.
I understand now, thank you.
Hello, I got a new error on a new session. For some reason, the code was unable to extract subject_id from the metadata.
Here is the error message:
Here is the error log:
And here are the contents of neurotensin_valence_convert_session.py: