I am getting a “VOLUME_COUNT_MISMATCH” bids validator error (v1.5.7 and v1.9.3) that I cannot figure out how to fix.
The error is being triggered by a diffusion sequence with a single direction. I have verified that the image file has only a single volume in dim4:
I have also checked that the associated bval and bvec files also only have entries for a single direction:
Everything seems to be lining up, so I’m at a loss as to what might be going on.
Thanks in advance,
This sounds like you are dealing with a b0-reference image. In that case, try renaming it with
_sbref.nii.gz/.json instead of
_dwi (but keep it in your
dwi/ folder). If that doesn’t work, try transpsing your b-vec (so it is in column form instead of rows or vice-versa).
Thanks for the suggestions. I had previously tried to transpose the bvec into 1 row x 3 columns, but that gave an error. So, the bvec file has to be 3 rows x 1 column (where columns = # diffusion directions and rows = x, y, z).
I also just tried renaming the .nii.gz and .json files to sbref instead of dwi, but it looks as if the bids standard doesn’t allow sbref for files in a dwi directory.
2: [ERR] Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder. (code: 1 - NOT_INCLUDED)
I’ll keep digging around to see if I can find a similar example anywhere. Worst case scenario, I just manually code the file into the .bidsignore.