-
Notifications
You must be signed in to change notification settings - Fork 8
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
Entities in CuBIDS.change_filename
are not comprehensive/up-to-date
#271
Comments
It's probably easier for the average CuBIDS user with BIDS noncompliant data to write a PyBIDS JSON config file than a set of BIDS schema files. However, PyBIDS is going to swap out its JSON-based config files for the BIDS schema files at some point, though I don't know when that'll actually happen. |
CuBIDS.change_filename
are not comprehensiveCuBIDS.change_filename
are not comprehensive/up-to-date
@mattcieslak BIDS makes the schema available as a single JSON file (https://bids-specification.readthedocs.io/en/stable/schema.json). I wonder if we could use that here. |
Hi all, after running
I was expecting any key found in the bids schema to pass through the apply step since these keys are retained in the RenameKeyGroup column of the |
Thanks @dabrielz! Agreed 100%. |
I was running
cubids-apply
on a dataset with complex-valued, multi-echo BOLD data, and it looks likeCuBIDS.change_filename
is not aware of certain entities, because those entities are not hardcoded into the function.In my case, it tried to rename
sub-03_ses-1_task-rest_acq-multiecho_run-02_echo-1_part-mag_bold.nii.gz
tosub-03_ses-1_task-rest_acq-multiechoVARIANTNumVolumes_run-002_bold.nii.gz
.We may want to grab config info from PyBIDS or the BIDS schema.
Of course, users may want to provide their own configuration files, in order to support entities or suffixes that are not yet covered by BIDS. In my case, I have
_noRF
files, which are associated with a currently open PR in the BIDS repo (bids-standard/bids-specification#1451).The text was updated successfully, but these errors were encountered: