Run parameter for Diffusion imaging

bids

#1

Hi,

We’ve run into an issue with the BIDS naming schema. We have been collecting multiple runs of diffusion imaging on our subjects within a single session. According to the standard BIDs specifications, _run- is not a valid option for diffusion data. Is it possible to include _run as a valid option for diffusion data? If not, any suggestions on how to deal with multiple runs?

Thanks,
Brian


#2

I just had a look at the spec and _run is definitely part of the spec for DWI data (see http://bids.neuroimaging.io/bids_spec1.1.0.pdf#page=24).

sub-<participant_label>/[ses-<session_label>/]
  dwi/
    sub-<participant_label>[_ses-<session_label>][_acq-<label>][_run-<index>]_dwi.nii[.gz]

What made you say run is not a valid option?


#3

Interesting. It’s not listed in Appendix IV as a valid option, and the online BIDS validator is giving us a naming error for all our diffusion data. Our files are names:
sub-_ses-_acq-_run-_dwi.nii.gz (example: sub-STELLA_ses-20180515_acq-DSIq5_run-1_dwi.nii.gz). The BIDs Validator is passing back the error: “Files with such naming scheme are not part of BIDS specification.”


#4

I fixed the table in the most recent draft - thanks for reporting.

I had a look at the validator code and this should work. What is the full path to the file that gives you issues?


#5

So I’m using the online validator with some local data on our servers. The local path is /projects/bruss/tmp_data/BIDS_warehouse/sub-STELLA/ses-20180515/diff/. Every file in that directory is passing back the same naming error.

I passed the BIDS_warehouse to the online validator (http://incf.github.io/bids-validator/)


#6

I see the problem now. Try renaming diff to dwi.


#7

Thanks that fixed the error. We’ll replicated that change into our converter and file structure.