Errors when running cubids apply with datalad

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

Screenshots / relevant information:



Hi @gabridele,

I just run cubids apply following the instructions in the Example Walkthrough and didn’t run into any issue.

If you also followed that Example and still encountered the same error, would you be able to share a minimally reproducible version of your data with me?

Best,
Tien

Hi @tientong,
Thank you for your answer. Yes, my workflow followed the one in the example walkthrough. However, I was wondering, could this issue arise from the fact that each of the subjects inside my datalad dataset is a datalad subdataset?

Best,
Gabriele

You’re correct that the Permission denied error you got is because each subject folder is a subdataset. cubids apply doesn’t support this. Also, this config (each subject as a subdataset) won’t work if you plan to use BABS later.

Hi @tientong, I understand now. Thanks a lot for your help!

Gabriele