I will need to save the running output from the terminal to a txt and get back to you on it, as the logs didn’t have everything from the terminal. And yes, I was only testing one subject out of the root directory, which contained 43 subjects. I used dcm2bids to parallel converted all of them so they should be the same across all subjects.
The BIDS validator seems to suggest that some subjects are missing files.
This is the log I got after rerunning the pipeline using the same command:
fmriprep_log.txt (360.6 KB)
It is still skipping the SDC for some reason.
Can you confirm the same files exist for the subject in this command which is different than the subject listed before? If the files exist, can you run a test on an earlier version of fmriprep and see if the error still happens?
Found out what the problem was - the mismatch between my testing participant in the command vs. in the folder! Sorry for the confusion. It’s now running now with the “i” capitalized and the URI removed. Thanks again for your help @Steven !