-
Notifications
You must be signed in to change notification settings - Fork 5
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Create example phenotypic inputs for no-session-layer BIDS case #100
Comments
We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 30 days. |
We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 30 days. |
We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 75 days.
|
@surchs I'm rereading this issue I created (quite a while ago) and would like a second opinion on whether this is still worth addressing. What gives me pause is the potential overhead related to adding these new examples: we will either need a test that runs both the bagel pheno and bagel bids commands, which seems kind of complex, or a new example JSONLD corresponding to another Wdyt? Do you think the intended handling of missing sessions in BIDS data is sufficiently covered by existing tests? |
At the moment, we have tests which check that:
PhenotypicSession
calledses-unnamed
is created by thebagel pheno
command when it receives a phenotypic TSV with missing session column valuesImagingSession
calledses-unnamed
(that has pipeline metadata) is created by thebagel derivatives
command when it receives a proc status TSV w/ missing session column valuesbagel bids
for a BIDS subject missing a session layer points to the BIDS subject directory (i.e., instead of inserting a fake session directory layer)What we don't have:
bagel bids
command that checks that when a BIDS directory with no session layer is provided, the output JSONLD file contains at least oneImagingSession
calledses-unnamed
, where the file path for the session still points to the subject directoryThis would test, explicitly, that
ses-unnamed
ImagingSessions are correctly created from BIDS datasets without sessions, and that the same sessions still have accurate paths to the data. At the moment, the combination of existing tests can be argued to test this implicitly.To be able to create the above test, we would need:
ds001
oreeg_ds000117
from `bids-examples)bagel bids
, that includes all subjects in the BIDS dataset abovea. a new valid phenotypic TSV with all subjects in the missing-session-layer BIDS dataset
b. a corresponding valid Neurobagel data dictionary JSON
Add to
tests/data
:The text was updated successfully, but these errors were encountered: