I’m in the process of converting a fairly large dataset into BIDS format, and have been trying to test in-house/adapted conversion tools piecemeal in order to ensure that each step will properly validate. I’ve been using this tool., which should be following the current BIDS spec. However, I’ve run into a few issues validating even simple subsets of our dataset.
The issues are the following:
Inheritance principle is not properly applied
I’ve tried including JSON files at the root, subject, and session level, named exactly according to the BIDS spec, to specify parameters (specifically “RepetitionTime” and “TaskName”) for multiple BOLD runs, but this has not worked. The validator throws three errors for each NIfTI file (JSON not formatted correctly, “RepetitionTime” not found, “TaskName” not found). It’s odd, as I’ve named this file exactly what the validator suggests, and have tried placing it at every point the validator suggests, but with no luck.
.bidsignore file not read
I’m using a version of dcm2bids to do conversion, which creates a folder named
tmp_dcm2bidsthat stores unmatched run names for each session converted. I created a file at the root level named
.bidsignore, per the BIDS spec, and included several variations of
tmp_dcm2bids/*to ignore, but the validator still reads the contents of
tmp_dcm2bidseach time and throws errors.
Has anyone else run into this same issue? I’ve tried many slight variations on placement and naming, none of which have worked. The setup follows the BIDS spec to the letter - I’d appreciate any advice if others have had this same problem, or if there might be a bug in the validator itself.
Thanks very much!
Austin Marcus, Carnegie Mellon University