RuntimeError: EchoTime2 metadata field not found. Please consult the BIDS specification.

[soichih]

I am trying to run fmriprep the OpenNeuro published dataset (like https://openneuro.org/datasets/ds001454)

The fmap data on this dataset seems to be stored in non-BIDS compatible format, and fmriprep fails with the following error message.

fMRIPrep failed: Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/legacymultiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 479, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 569, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 662, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 382, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/sdcflows/interfaces/fmap.py", line 204, in _run_interface
    _delta_te(self.inputs.metadata),
  File "/usr/local/miniconda/lib/python3.7/site-packages/sdcflows/interfaces/fmap.py", line 529, in _delta_te
    'EchoTime2 metadata field not found. Please consult the BIDS specification.')
RuntimeError: EchoTime2 metadata field not found. Please consult the BIDS specification.

The EchoTime1/2 are basically stored under magnitude1.json and magnitude2.json respectively, and on phasediff.json, it just has "EchoTime" (from magnitude2). According to BIDS specification, EchoTime1/2 should be stored on phasediff.json, and there should be no magnitude1/2.json.

I think I can pursuit several options...

1. Run fmriprep without fmap
2. Download the dataset, modify the fmap json manually, and run fmriprep
3. Have fmriprep updated so that it will look for magnitude1/2.json if EchoTime1/2 are not specified in the phasediff.json - although it's not BIDS compatible..
4. OpenNeuro will run BIDS validator on older datasets and correct issues if it fails to validate?

What would you recommend me to do?

[kimsin98]

Editing phasediff.json files should be the right approach. Batch editing JSON files is simple if you use bash (jq) or python (json module)

[oesteban]

Related to #64.

[oesteban]

The dataset has been fixed on OpenNeuro. Please reopen if this is still an issue.

Moreover, the upcoming version 1.4.0 of SDCFlows will be much more thorough in testing the availability of all necessary metadata early.