aramis-lab / clinica

Software platform for clinical neuroimaging studies
http://www.clinica.run/
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Store source identifiers in BIDS metadata during conversion #588

Open ghisvail opened 2 years ago

ghisvail commented 2 years ago

Whilst reviewing #587, it struck me that some parts of Clinica implement conversions from BIDS normalized IDs back to the source dataset IDs for subjects and sessions. It's probably not the only place where this is done, which leads to the potential for accidental code duplication of dataset-specific logic.

One solution to this would be to just store the source subject and session IDs in their respective metadata files, such as:

participants.tsv:

participant_id source_participant_id group age sex
sub-ADNI011S0002 011_S_0002 control 22 F

sub-<label>_sessions.tsv:

session_id source_session_id medhist* npi*
ses-M00 bl n/a n/a

This way we could assume that any dataset converted using Clinica provides source IDs systematically and consistently.

github-actions[bot] commented 2 years ago

This issue is considered stale because it has not received further activity for the last 14 days. You may remove the inactive label or add a comment, otherwise it will be closed after the next 14 days.

github-actions[bot] commented 2 years ago

This issue is considered stale because it has not received further activity for the last 14 days. You may remove the inactive label or add a comment, otherwise it will be closed after the next 14 days.

github-actions[bot] commented 2 years ago

This issue is considered stale because it has not received further activity for the last 14 days. You may remove the inactive label or add a comment, otherwise it will be closed after the next 14 days.

github-actions[bot] commented 1 year ago

This issue is considered stale because it has not received further activity for the last 14 days. You may remove the inactive label or add a comment, otherwise it will be closed after the next 14 days.

github-actions[bot] commented 1 year ago

This issue is considered stale because it has not received further activity for the last 14 days. You may remove the inactive label or add a comment, otherwise it will be closed after the next 14 days.

github-actions[bot] commented 1 year ago

This issue is considered stale because it has not received further activity for the last 14 days. You may remove the inactive label or add a comment, otherwise it will be closed after the next 14 days.

github-actions[bot] commented 1 year ago

This issue is considered stale because it has not received further activity for the last 14 days. You may remove the inactive label or add a comment, otherwise it will be closed after the next 14 days.

github-actions[bot] commented 9 months ago

This issue is considered stale because it has not received further activity for the last 14 days. You may remove the inactive label or add a comment, otherwise it will be closed after the next 14 days.

github-actions[bot] commented 6 months ago

This issue is considered stale because it has not received further activity for the last 14 days. You may remove the inactive label or add a comment, otherwise it will be closed after the next 14 days.

NicolasGensollen commented 6 months ago

@AliceJoubert, again, no rush but also worth taking a look at this when you have some time.

github-actions[bot] commented 3 months ago

This issue is considered stale because it has not received further activity for the last 14 days. You may remove the inactive label or add a comment, otherwise it will be closed after the next 14 days.