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DCAN-Labs / abcd-hcp-pipeline

bids application for processing functional MRI data, robust to scanner, acquisition and age variability.
https://hub.docker.com/r/dcanumn/abcd-hcp-pipeline
BSD 3-Clause "New" or "Revised" License
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bug: BIDS App expects AcquisitionMatrixPE metadata in get_realdwelltime function, even in the absence of fieldmaps #17

Closed uriartel closed 8 months ago

uriartel commented 5 years ago

A bug was found that is preventing the BIDS app to run on the ABIDE dataset. The information in the json files for the ABIDE data is different than that of the ABCD dataset. The ABIDE json files are organized using "AcquisitionMatrix" where as the ABCD json files uses "AcquisitionMatrixPE".

Example for ABIDE "AcquisitionMatrix": "80x64",

Example for ABCD "AcquisitionMatrixPE": 90,

Due to this difference the BIDS app can not be run on the ABIDE dataset. The ABIDE json files may need to be converted, or the script can be adjusted in order to compensate the difference of the json files.

ericearl commented 5 years ago

@uriartel Can you please paste just the Python traceback from your error log that had the relevant lines in helpers.py, etc.?

dasturge commented 5 years ago

There are two fixes for this. Firstly, we can change the logic in the ParameterSettings class to only check for this metadata in the presence of FieldMaps. The second, is to write flexible logic to read the nPE steps from either of these json fields. We should do both.

uriartel commented 5 years ago

Traceback (most recent call last): File "/app/run.py", line 364, in _cli() File "/app/run.py", line 67, in _cli return interface(**kwargs) File "/app/run.py", line 263, in interface session_spec = ParameterSettings(session, out_dir) File "/app/pipelines.py", line 106, in init self.bids_data['t1w_metadata']) File "/app/helpers.py", line 196, in get_realdwelltime num_steps = metadata['AcquisitionMatrixPE'] KeyError: 'AcquisitionMatrixPE'

I believe that these are the relevant lines.

LuciMoore commented 8 months ago

It appears that the issue might have been addressed implicitly through subsequent updates, changes, or improvements. Since there hasn't been any recent activity or confirmation regarding its relevance, we are considering this issue resolved.

If you believe the matter is still relevant or requires further attention, please feel free to reopen the issue, and we'll be more than happy to revisit and address it promptly.