Dcm2bids version 3.1.0 intended for field

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1

The updated version of dcm2bids (version 3/1/0) is adding a “bids::” before the actual location of the functional MRI scan in the IntendedForField. When this is added, fMRIprep can’t find our distortion scan. Is there a simple solution for this that doesn’t involve our having to update the json file with a script?

For example,

dcm2bids 3.1.0 is outputting (here fMRIprep can’t find the distortion scan)

“IntendedFor”: “bids::sub-0001/ses-01/dwi/sub-0001_ses-01_acq-90d_dir-AP_dwi.nii.gz”,

old dcm2bids was outputting and this works with fMRIprep
“IntendedFor”: “sub-0001/ses-01/dwi/sub-0001_ses-01_acq-90d_dir-AP_dwi.nii.gz”,

2

Hi,

This is a similar discussion on the same issue:

3

Hi @AustinBipolar,

In short, no. But a python script with the json package should solve your issue easily. Also, fMRIPrep should eventually honor the BIDS URI, which would no longer produce the error. Additionally, we are thinking of having dcm2bids instead output B0FieldSource/Identifier pairs in a future release.

Also,

The correct version without the BIDS URI should not have sub-0001/ in front.

Best,
Steven

4

Not super helpful to anybody right now, but the next release will have experimental support for BIDS-URIs.

5

Ok thanks very much! We will go with a script to change.