`.snakebids` file not found

I performed a dry run of the Docker as per the instructions on the Hippunfold Installation instructions and ran into an error (see screenshot below).

It seems that the app “.snakebids” is required in the out directory but I am not sure how to do that. I am new to using a BIDS App like Hippunfold, so some guidance on this would be really helpful.

The CLI code that I used is below:

I have created an issue for this in GitHub as well.

It’s my first time posting in this forum. Let me know if this post belongs some place else. Also, if you require further information, please let me know.


Usually it is bad practice to use the same directory as input and output. Outputs should be placed in the “derivatives” folder in your BIDS root. Try doing that and see if it makes a difference.


According to the GitHub thread they fixed the error of .snakebids not being created in directories that already exist, but you should still specify that outputs go in to the derivatives folder.