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BrkRaw / brkraw

BrkRaw: A comprehensive tool to access raw Bruker Biospin MRI data
https://brkraw.github.io
GNU General Public License v3.0
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Bids_helper quits when method file is missing #145

Open mschneider1711 opened 9 months ago

mschneider1711 commented 9 months ago

Describe the bug The bids_helper catches an error when the dataset doesn't contain a method file. Even if this is the right behaviour, the script shouldn't break there if I want to convert many datasets to bids at the same time. It should rather neglect the scan without the method file and continue running for the rest.

The exact error catches where the method of the scan needs to be read out. In brkraw.py line 319-320: if not is_localizer(dset, scan_id, reco_id): method = dset.get_method(scan_id).parameters['Method']

To Reproduce Steps to reproduce the behavior: Run the bids_helper on a to nifti converted dataset which doesn't have a method file.

Expected behavior The scan without the method file should be neglected and the script should continue running.

dvm-shlee commented 9 months ago

Hi @mschneider1711,

Thank you for your input. We're aware of this issue, along with other BIDS helper crashes linked to unexpected scenarios in single scan data. Rest assured, these will be addressed in the next update. Until then, the simplest workaround is to delete the folder causing the problem from the dataset.