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Technical: BIDS validator errors #7

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opened 2025-05-22 15:46:00 +00:00 by msz · 0 comments
msz commented 2025-05-22 15:46:00 +00:00
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For the current conversion, the bids validator reports several warnings (mostly SIDECAR_KEY_RECOMMENDED), but also two errors:

Extension mismatch

[ERROR] EXTENSION_MISMATCH Extension used by file does not match allowed extensions for its suffix
                /sub-f/dwi/sub-f_acq-b1200_sbref.bval
                /sub-f/dwi/sub-f_acq-mshell_sbref.bval

                10 more files with the same issue

This has been flagged in #1 and needs clarification about the intended meaning of these acquisitions.

Repetition Time / Acquisition Duration

[ERROR] REPETITION_TIME_AND_ACQUISITION_DURATION_MUTUALLY_EXCLUSIVE The fields 'RepetitionTime' and 'AcquisitionDuration' for this file are mutually exclusive.
To specify acquisition duration, use 'SliceTiming' or 'DelayTime'
(RepetitionTime - AcquisitionDuration).

The sidecar JSONs are produced by dcm2niix (with potential postprocessing by Heudiconv). The functional images all have RepetitionTime 1.5 seconds, but the AcquisitionDuration values are (closest multiples of 1.5 in brackets): 719.42 (720), 481.417 (481.5), 727.417 (727.5), 44.417 (45). This means rounding is required to either half-second or full second. I am currently not sure whether that is a data issue, dcm2niix issue, or heudiconv issue.

For the current conversion, the bids validator reports several warnings (mostly SIDECAR_KEY_RECOMMENDED), but also two errors: ### Extension mismatch ``` [ERROR] EXTENSION_MISMATCH Extension used by file does not match allowed extensions for its suffix /sub-f/dwi/sub-f_acq-b1200_sbref.bval /sub-f/dwi/sub-f_acq-mshell_sbref.bval 10 more files with the same issue ``` This has been flagged in #1 and needs clarification about the intended meaning of these acquisitions. ### Repetition Time / Acquisition Duration ``` [ERROR] REPETITION_TIME_AND_ACQUISITION_DURATION_MUTUALLY_EXCLUSIVE The fields 'RepetitionTime' and 'AcquisitionDuration' for this file are mutually exclusive. To specify acquisition duration, use 'SliceTiming' or 'DelayTime' (RepetitionTime - AcquisitionDuration). ``` The sidecar JSONs are produced by dcm2niix (with potential postprocessing by Heudiconv). The functional images all have `RepetitionTime` 1.5 seconds, but the `AcquisitionDuration` values are (closest multiples of 1.5 in brackets): 719.42 (720), 481.417 (481.5), 727.417 (727.5), 44.417 (45). This means rounding is required to either half-second or full second. I am currently not sure whether that is a data issue, dcm2niix issue, or heudiconv issue.
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q02/phantom-mri-bids#7
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