KeyError: 'DwellTime' about hcppipelines HOT 7 OPEN

It looks like the JSON sidecar associated with the T1w you are trying to process does not have a 'DwellTime' field. The DwellTime value is required for correcting distortion in the anatomicals. The best solution would be to identify this value and add the field to your JSON file, which you get from DICOM field (0019,1018) / 1e-6. For Siemens, 1/(PixelBandwidth * BaseResolution* ParallelReductionFactorInPlane) might give you right value, if you happen to have those fields in the JSON.

If you are running the pipeline in --processing_mode legacy, without distortion correction, this value isn't needed. I'll update the code to handle this case more gracefully, but an immediate workaround would be to add something like "DwellTime": 0 to your JSON (taking care not to share your BIDS data with this invalid field!)

from hcppipelines.

@rhancockn Add error handling around t1_spacing = layout.get_metadata(t1ws[0])["DwellTime"] (and maybe t2_spacing = layout.get_metadata(t2ws[0])["DwellTime"]). If distortion correction is to be done, throw a descriptive error message about why this field is required. Otherwise, set t1_spacing = 'NONE'.

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Thank you @rhancockn. So if I want to run --processing-mode hcp I'd always need the DwellTime value? Is --processing-mode hcp the default?

from hcppipelines.

from hcppipelines.

Hiya! I've been trying to run this BIDs/HCP app (https://hub.docker.com/r/bids/hcppipelines) using the dataset from this tutorial (https://bids-apps.neuroimaging.io/tutorial/), and have run into the same error. However, I don't have any access to a JSON file similar to what you've described, despite downloading the tutorial dataset. Is there something I can do to work around this, or am I missing something?

from hcppipelines.

It looks like the JSON sidecar associated with the T1w you are trying to process does not have a 'DwellTime' field. The DwellTime value is required for correcting distortion in the anatomicals. The best solution would be to identify this value and add the field to your JSON file, which you get from DICOM field (0019,1018) / 1e-6. For Siemens, 1/(PixelBandwidth * BaseResolution* ParallelReductionFactorInPlane) might give you right value, if you happen to have those fields in the JSON.

If you are running the pipeline in --processing_mode legacy, without distortion correction, this value isn't needed. I'll update the code to handle this case more gracefully, but an immediate workaround would be to add something like "DwellTime": 0 to your JSON (taking care not to share your BIDS data with this invalid field!)

I tried that but run.py is still complaining about the missing key....

from hcppipelines.

This is still an issue in docker://bids/hcppipelines:v4.3.0-3 , even with --processing_mode legacy. Setting DwellTime to 0 does serve as a workaround.

from hcppipelines.