Summary of what happened:
Hi all,
I have a question about using cubids apply . I am curating an MRI dataset that is BIDS-compliant and version-controlled with the help of DataLad. I am now trying to apply the changes identified by the cubids group command, but I am struggling because I keep encountering errors related to my use of DataLad. Specifically, I get a “permission denied” error whenever it tries to rename files because they need to be unlocked. If I unlock them before running the code, I get an error claiming the dataset is not “clean.”
However, I have to use the --use-datalad flag since I am dealing with symlinks rather than actual files, so git mv should be used instead of a simple mv when renaming.
Here are some screenshots from my command line. In the first screenshot, the command is wrapped with datalad run ; in the second picture, I also tried running the cubids apply command alone.
Command used (and if a helper script was used, a link to the helper script or the command generated):
See screenshots below
Version:
cubids v1.2.1.dev5+g0be1b9a
Environment (Docker, Singularity / Apptainer, custom installation):
CuBIDS was installed via git cloning the github repository
Data formatted according to a validatable standard? Please provide the output of the validator:
Data is BIDS-compliant
