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spatialtopology / spacetop-prep

code for transferring data and preprocessing
MIT License
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[DUP] BIDS validator issue 02: IntendedFor for deleted dup files #87

Open jungheejung opened 1 month ago

jungheejung commented 1 month ago

TODO

fmriprep output


    2: [ERR] 'IntendedFor' field needs to point to an existing file. (code: 37 - INTENDED_FOR)
        ./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

(Insert scannotes from ST_participants)

jungheejung commented 1 month ago

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