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[DUP] BIDS validator issue 02: IntendedFor for deleted dup files #87

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jungheejung opened this issue May 29, 2024 · 1 comment
Open
1 task

[DUP] BIDS validator issue 02: IntendedFor for deleted dup files #87

jungheejung opened this issue May 29, 2024 · 1 comment

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@jungheejung
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TODO

  • ISSUE: __dup files are deleted, but they linger in IntendedFor fields
  • remove __dup filenames in IntendeFor. OR repopulate intendedFor with new dataset

fmriprep output


	�[31m2: [ERR] 'IntendedFor' field needs to point to an existing file. (code: 37 - INTENDED_FOR)�[39m
		./sub-0011/ses-01/fmap/sub-0011_ses-01_acq-96dirX6b0Xmb_dir-ap_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0011/ses-01/fmap/sub-0011_ses-01_acq-96dirX6b0Xmb_dir-ap_epi.nii.gz') does not point to an existing file('ses-01/dwi/sub-0011_ses-01_acq-96dirX6b0Xmb_dwi__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0011/').
			Evidence: ses-01/dwi/sub-0011_ses-01_acq-96dirX6b0Xmb_dwi__dup-01.nii.gz
		./sub-0011/ses-01/fmap/sub-0011_ses-01_acq-96dirX6b0Xmb_dir-pa_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0011/ses-01/fmap/sub-0011_ses-01_acq-96dirX6b0Xmb_dir-pa_epi.nii.gz') does not point to an existing file('ses-01/dwi/sub-0011_ses-01_acq-96dirX6b0Xmb_dwi__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0011/').
			Evidence: ses-01/dwi/sub-0011_ses-01_acq-96dirX6b0Xmb_dwi__dup-01.nii.gz
		./sub-0018/ses-04/fmap/sub-0018_ses-04_acq-mb8_dir-ap_run-02_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0018/ses-04/fmap/sub-0018_ses-04_acq-mb8_dir-ap_run-02_epi.nii.gz') does not point to an existing file('ses-04/func/sub-0018_ses-04_task-alignvideo_acq-mb8_run-01_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0018/').
			Evidence: ses-04/func/sub-0018_ses-04_task-alignvideo_acq-mb8_run-01_bold__dup-01.nii.gz
		./sub-0018/ses-04/fmap/sub-0018_ses-04_acq-mb8_dir-ap_run-02_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0018/ses-04/fmap/sub-0018_ses-04_acq-mb8_dir-ap_run-02_epi.nii.gz') does not point to an existing file('ses-04/func/sub-0018_ses-04_task-alignvideo_acq-mb8_run-01_sbref__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0018/').
			Evidence: ses-04/func/sub-0018_ses-04_task-alignvideo_acq-mb8_run-01_sbref__dup-01.nii.gz
		./sub-0018/ses-04/fmap/sub-0018_ses-04_acq-mb8_dir-pa_run-02_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0018/ses-04/fmap/sub-0018_ses-04_acq-mb8_dir-pa_run-02_epi.nii.gz') does not point to an existing file('ses-04/func/sub-0018_ses-04_task-alignvideo_acq-mb8_run-01_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0018/').
			Evidence: ses-04/func/sub-0018_ses-04_task-alignvideo_acq-mb8_run-01_bold__dup-01.nii.gz
		./sub-0018/ses-04/fmap/sub-0018_ses-04_acq-mb8_dir-pa_run-02_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0018/ses-04/fmap/sub-0018_ses-04_acq-mb8_dir-pa_run-02_epi.nii.gz') does not point to an existing file('ses-04/func/sub-0018_ses-04_task-alignvideo_acq-mb8_run-01_sbref__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0018/').
			Evidence: ses-04/func/sub-0018_ses-04_task-alignvideo_acq-mb8_run-01_sbref__dup-01.nii.gz
		./sub-0024/ses-01/fmap/sub-0024_ses-01_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0024/ses-01/fmap/sub-0024_ses-01_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-01/func/sub-0024_ses-01_task-social_acq-mb8_run-02_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0024/').
			Evidence: ses-01/func/sub-0024_ses-01_task-social_acq-mb8_run-02_bold__dup-01.nii.gz
		./sub-0024/ses-01/fmap/sub-0024_ses-01_acq-mb8_dir-pa_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0024/ses-01/fmap/sub-0024_ses-01_acq-mb8_dir-pa_run-01_epi.nii.gz') does not point to an existing file('ses-01/func/sub-0024_ses-01_task-social_acq-mb8_run-02_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0024/').
			Evidence: ses-01/func/sub-0024_ses-01_task-social_acq-mb8_run-02_bold__dup-01.nii.gz
		./sub-0024/ses-03/fmap/sub-0024_ses-03_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0024/ses-03/fmap/sub-0024_ses-03_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-03/func/sub-0024_ses-03_task-social_acq-mb8_run-05_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0024/').
			Evidence: ses-03/func/sub-0024_ses-03_task-social_acq-mb8_run-05_bold__dup-01.nii.gz
		./sub-0024/ses-03/fmap/sub-0024_ses-03_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0024/ses-03/fmap/sub-0024_ses-03_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-03/func/sub-0024_ses-03_task-social_acq-mb8_run-05_sbref__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0024/').
			Evidence: ses-03/func/sub-0024_ses-03_task-social_acq-mb8_run-05_sbref__dup-01.nii.gz
		./sub-0024/ses-03/fmap/sub-0024_ses-03_acq-mb8_dir-pa_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0024/ses-03/fmap/sub-0024_ses-03_acq-mb8_dir-pa_run-01_epi.nii.gz') does not point to an existing file('ses-03/func/sub-0024_ses-03_task-social_acq-mb8_run-05_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0024/').
			Evidence: ses-03/func/sub-0024_ses-03_task-social_acq-mb8_run-05_bold__dup-01.nii.gz
		./sub-0024/ses-03/fmap/sub-0024_ses-03_acq-mb8_dir-pa_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0024/ses-03/fmap/sub-0024_ses-03_acq-mb8_dir-pa_run-01_epi.nii.gz') does not point to an existing file('ses-03/func/sub-0024_ses-03_task-social_acq-mb8_run-05_sbref__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0024/').
			Evidence: ses-03/func/sub-0024_ses-03_task-social_acq-mb8_run-05_sbref__dup-01.nii.gz
		./sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0025_ses-02_task-faces_acq-mb8_run-02_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0025/').
			Evidence: ses-02/func/sub-0025_ses-02_task-faces_acq-mb8_run-02_bold__dup-01.nii.gz
		./sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0025_ses-02_task-faces_acq-mb8_run-02_sbref__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0025/').
			Evidence: ses-02/func/sub-0025_ses-02_task-faces_acq-mb8_run-02_sbref__dup-01.nii.gz
		./sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0025_ses-02_task-narratives_acq-mb8_run-01_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0025/').
			Evidence: ses-02/func/sub-0025_ses-02_task-narratives_acq-mb8_run-01_bold__dup-01.nii.gz
		./sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0025_ses-02_task-narratives_acq-mb8_run-01_sbref__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0025/').
			Evidence: ses-02/func/sub-0025_ses-02_task-narratives_acq-mb8_run-01_sbref__dup-01.nii.gz
		./sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0025_ses-02_task-faces_acq-mb8_run-02_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0025/').
			Evidence: ses-02/func/sub-0025_ses-02_task-faces_acq-mb8_run-02_bold__dup-01.nii.gz
		./sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0025_ses-02_task-faces_acq-mb8_run-02_sbref__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0025/').
			Evidence: ses-02/func/sub-0025_ses-02_task-faces_acq-mb8_run-02_sbref__dup-01.nii.gz
		./sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0025_ses-02_task-narratives_acq-mb8_run-01_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0025/').
			Evidence: ses-02/func/sub-0025_ses-02_task-narratives_acq-mb8_run-01_bold__dup-01.nii.gz
		./sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0025/ses-02/fmap/sub-0025_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0025_ses-02_task-narratives_acq-mb8_run-01_sbref__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0025/').
			Evidence: ses-02/func/sub-0025_ses-02_task-narratives_acq-mb8_run-01_sbref__dup-01.nii.gz
		./sub-0034/ses-04/fmap/sub-0034_ses-04_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0034/ses-04/fmap/sub-0034_ses-04_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-04/func/sub-0034_ses-04_task-fractional_acq-mb8_run-01_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0034/').
			Evidence: ses-04/func/sub-0034_ses-04_task-fractional_acq-mb8_run-01_bold__dup-01.nii.gz
		./sub-0034/ses-04/fmap/sub-0034_ses-04_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0034/ses-04/fmap/sub-0034_ses-04_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-04/func/sub-0034_ses-04_task-fractional_acq-mb8_run-01_sbref__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0034/').
			Evidence: ses-04/func/sub-0034_ses-04_task-fractional_acq-mb8_run-01_sbref__dup-01.nii.gz
		./sub-0034/ses-04/fmap/sub-0034_ses-04_acq-mb8_dir-pa_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0034/ses-04/fmap/sub-0034_ses-04_acq-mb8_dir-pa_run-01_epi.nii.gz') does not point to an existing file('ses-04/func/sub-0034_ses-04_task-fractional_acq-mb8_run-01_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0034/').
			Evidence: ses-04/func/sub-0034_ses-04_task-fractional_acq-mb8_run-01_bold__dup-01.nii.gz
		./sub-0034/ses-04/fmap/sub-0034_ses-04_acq-mb8_dir-pa_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0034/ses-04/fmap/sub-0034_ses-04_acq-mb8_dir-pa_run-01_epi.nii.gz') does not point to an existing file('ses-04/func/sub-0034_ses-04_task-fractional_acq-mb8_run-01_sbref__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0034/').
			Evidence: ses-04/func/sub-0034_ses-04_task-fractional_acq-mb8_run-01_sbref__dup-01.nii.gz
		./sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0036/').
			Evidence: ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_bold__dup-01.nii.gz
		./sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_bold__dup-02.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0036/').
			Evidence: ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_bold__dup-02.nii.gz
		./sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_sbref__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0036/').
			Evidence: ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_sbref__dup-01.nii.gz
		./sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_sbref__dup-02.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0036/').
			Evidence: ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_sbref__dup-02.nii.gz
		./sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0036/').
			Evidence: ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_bold__dup-01.nii.gz
		./sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_bold__dup-02.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0036/').
			Evidence: ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_bold__dup-02.nii.gz
		./sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_sbref__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0036/').
			Evidence: ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_sbref__dup-01.nii.gz
		./sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0036/ses-02/fmap/sub-0036_ses-02_acq-mb8_dir-pa_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_sbref__dup-02.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0036/').
			Evidence: ses-02/func/sub-0036_ses-02_task-narratives_acq-mb8_run-01_sbref__dup-02.nii.gz
		./sub-0038/ses-02/fmap/sub-0038_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0038/ses-02/fmap/sub-0038_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0038_ses-02_task-narratives_acq-mb8_run-01_bold__dup-01.nii.gz'). Please mind that this value should not include subject level directory ('/sub-0038/').
			Evidence: ses-02/func/sub-0038_ses-02_task-narratives_acq-mb8_run-01_bold__dup-01.nii.gz
		./sub-0038/ses-02/fmap/sub-0038_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz
			'IntendedFor' property of this fieldmap  ('/sub-0038/ses-02/fmap/sub-0038_ses-02_acq-mb8_dir-ap_run-01_epi.nii.gz') does not point to an existing file('ses-02/func/sub-0038_ses-02_task-narratives_acq-mb8_run-01_sbref__dup-

scannotes

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@jungheejung
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@yarikoptic If there is a script to remove dups in IntendedFor fields, please go ahead and run it

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