fMRIprep 1.2.3: KeyError: 'RepetitionTime'

1

Hi again! Just a reminder that I’m totally new to this and still figuring out bash etc.
Have been working on running fMRIprep 1.2.3. and am now receiving this error:

self.run()
File “/usr/local/miniconda/lib/python3.6/multiprocessing/process.py”, line 93$
self._target(*self._args, **self._kwargs)
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, $
ignore_aroma_err=opts.ignore_aroma_denoising_errors,
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/bas$
ignore_aroma_err=ignore_aroma_err,
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/bas$
num_bold=len(subject_data[‘bold’]))
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/bol$
name=‘carpetplot_wf’)
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/bol$
tr=metadata[‘RepetitionTime’],
KeyError: ‘RepetitionTime’

I already tried
find $BIDS_DIR -name ‘_bold.’
find $BIDS_DIR -name ‘*_bold.json’ -exec grep RepetitionTime “{}” +

and got the same error. Thanks again!

2

Hi @knameth !

Just to get a little more detail – how are you running fMRIPrep ? Specifically, are you running the BIDS validator on your input files ? It looks like the error is suggesting that you don’t have a RepetitionTime key defined in your json sidecar, which is a required field for BOLD files.

HTH,

Elizabeth

1 Like
3

Hi @knameth,

Could you show the BIDS structure for one subject? Or, alternatively, post the full output of fmriprep