Summary of what happened:
Hello,
I’m having some strange issues with bids validation (online tool and when trying to run fmriprep). I ran fmriprep successfully on monday, and then added a new subject to my BIDS folder yesterday and now I’m getting many warnings and an error across all the subjects I have. It seems like the bids validator is not properly reading information from nifi headers among other issues.
Issue reading BIDSVersion::
The BIDSVersion field of 'dataset_description.json' does not match a known release. The BIDS Schema used for validation may be out of date.
My dataset_description.json file is {"Name": "Trimodal EEG,fMRI,PET dataset", "BIDSVersion": "1.4.0"}
I tried also “BIDSVersion”:“1.3.0” and received the same message.
Issue Reading Headers:
NIfTI file's header field for dimension information is blank or too short.
/sub-racsleep35/anat/sub-racsleep35_run-001_T1w.nii.gz
/sub-racsleep35/func/sub-racsleep35_task-rest_run-001_bold.nii.gz
/sub-racsleep32/func/sub-racsleep32_task-rest_run-001_bold.nii.gz
/sub-racsleep32/anat/sub-racsleep32_run-001_T1w.nii.gz
/sub-racsleep38/anat/sub-racsleep38_run-001_T1w.nii.gz
/sub-racsleep38/func/sub-racsleep38_task-rest_run-001_bold.nii.gz
/sub-racsleep36/func/sub-racsleep36_task-rest_run-001_bold.nii.gz
/sub-racsleep36/anat/sub-racsleep36_run-001_T1w.nii.gz
racsleep38 is the new subject, and none of the others flagged any issues when run on monday.
These files all seem to have valid headers when I run commands like fslinfo or when I manually extract header information using the bids library in python:
bold_imgs = layout.get(suffix='bold',extension=[".nii.gz"]
bold_imgs[0].get_image().header.get_zooms()
^ this returns the dimensions / resolutions that match the .json sidecar files perfectly.
I think because it’s not reading headers properly, I end up with an actual error saying the Repetition Time doesn’t match, but I think it’s just not reading the header properly at all.
Happy to hear any suggestions anyone has! I can just run fmriprep bypassing BIDS validation, but I wanted to flag this as an issue in case anyone else experiences it.
- Harris