Comments (3)
rhancockn
commented on June 14, 2024
From the output, it looks like you are using an older version of the container (pre 4.1.3). The 4.1.3 version can currently be pulled from rhancock/hcpbids on DockerHub. Sorry about this-I know there are some inconsistencies in which container to pull, which I will soon correct. I tested the older bids/hcppipelines on a sample tree and can reproduce your error, but the validation step succeeds on the newer rhancock/hcpbids image. The files you list do have valid BIDS names, so it remains a mystery why validation fails with the older version. There is also a --skip_bids_validation flag to the container.
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annchenknodt
commented on June 14, 2024
Ah, thanks for clearing that up and for all your work on this! I did get past validation after I re-built my singularity container from rhancock/hcpbids, but hit another error pretty quickly. I have a thread going on neurorstars with details on that so I'll just link to it rather than duplicate here: https://neurostars.org/t/processing-hcp-aging-dataset-in-bids-format/15164/4
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rhancockn
commented on June 14, 2024
Closing to continue discussion on neurostars.
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Related Issues (20)
- Implement LegacyStyleData HOT 1
- No T2w files found for sub-{subject_label}. Consider --procesing_mode [legacy | auto ]. HOT 6
- BIDs validation fails inside container on previously validated dataset
- Validate stage options
- Check file existence
- Reduce the size of the Docker image
- Python type error HOT 1
- KeyError: 'DwellTime' HOT 7
- BIDs issue- 'BIDS root does not exist' HOT 4
- BIDS App wrapper for HCP Pipelines v4.3.0
- ERROR: crypt() returned null with 4-line file HOT 6
- wb_command not installed in container
- PostFreeSurferPipeline.sh: ERROR: unrecognized option: '--printcom'
- fieldmap for BOLD file not found even though it is present HOT 4
- ICA-FIX implementation for BIDS
- PostFreeSurferPipeline error
- Running FAST segmentation Exception: Not enough classes detected to init KMeans HOT 8
- fail to run latest image in CI
- test data failing HOT 2
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