Summary of what happened:
Files do not meet BIDS spec. Aiming to rename them using image orrientation and phase encoding direction from the json file.
Version:
“ConversionSoftware”: “dcm2niix”,
“ConversionSoftwareVersion”: “v1.0.20241211”,
Data formatted according to a validatable standard? Please provide the output of the validator:
Aiming to meet BIDS standard, currently have
error: NOT_INCLUDED
- /sub-FADFMRI100/ses-1/fmap/sub-FADFMRI100_ses-1_task-rest_run-001_bold-revPE.json
- /sub-FADFMRI100/ses-1/fmap/sub-FADFMRI100_ses-1_task-rest_run-001_bold-revPE.nii.gz
And many other files have the same error too.
Screenshots / relevant information:
Hi, I’m a beginner to neuroimaging analysis.
I wanted to check how phase direction works in fmap scans for BIDS datasets.
I have a dataset that looks like it has been converted using dcm2niix, and is now in a BIDS format.
The fieldmap files don’t meet the BIDS spec, so I am working out how to change them so that they do.
The fmap file names are written like sub-FADFMRI100_ses-1_task-rest_run-001_bold-revPE.nii.gz
It looks like it should be
sub-FADFMRI100_ses-1_task-rest_run-001_dir-AP_epi.nii.gz
It looks like the fmap files are the 4th option here, so I need the phase encoding direction for the file name.
This is a long way of asking, if I have the PhaseEncodingDirection (in the json file) and the image orientation (eg LAS, RPI, which I can get from the nifti file header), does this uniquely define the alphanumeric label phase encoding direction that needs to be in the filename? Is there more data I would need to use?
I wonder if it is related to this bug, bids.BIDSLayout.build_path() discards dir- label for dwi images · Issue #895 · bids-standard/pybids · GitHub , although I’m looking at fMRI not DWI.
Thanks for your help!