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spatialtopology / spacetop-prep

code for transferring data and preprocessing
MIT License
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[DUP] BIDS validator issue 04: weirdly renamed dups #89

Closed jungheejung closed 4 months ago

jungheejung commented 4 months ago

TODO

fmriprep output

    4: [ERR] acq Name contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec. (code: 59 - ACQ_NAME_CONTAIN_ILLEGAL_CHARACTER)
        ./sub-0025/ses-03/func/sub-0025_ses-03_task-social_acq-mb8_51_run-03_bold.json
            acq Name contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec.
            Evidence: acq name contains illegal character:/sub-0025/ses-03/func/sub-0025_ses-03_task-social_acq-mb8_51_run-03_bold.json
        ./sub-0025/ses-03/func/sub-0025_ses-03_task-social_acq-mb8_51_run-03_events.tsv
            acq Name contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec.
            Evidence: acq name contains illegal character:/sub-0025/ses-03/func/sub-0025_ses-03_task-social_acq-mb8_51_run-03_events.tsv
        ./sub-0025/ses-03/func/sub-0025_ses-03_task-social_acq-mb8_51_run-03_sbref.nii.gz
            acq Name contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec.
            Evidence: acq name contains illegal character:/sub-0025/ses-03/func/sub-0025_ses-03_task-social_acq-mb8_51_run-03_sbref.nii.gz

scannotes

(Insert scannotes from ST_participants)

jungheejung commented 4 months ago

./sub-0025/ses-03/func/sub-0025_ses-03_task-social_acq-mb8_51_run-03_bold.json is PRIMARY

grep '"AcquisitionTime": "' ./sub-0025/ses-03/func/sub-0025_ses-03_task-social_acq-mb8*run-03_bold.json 
./sub-0025/ses-03/func/sub-0025_ses-03_task-social_acq-mb8_51_run-03_bold.json:  "AcquisitionTime": "12:00:0.652500",
./sub-0025/ses-03/func/sub-0025_ses-03_task-social_acq-mb8_run-03_bold.json:  "AcquisitionTime": "11:53:40.867500",

nib-ls ./sub-0025/ses-03/func/sub-0025_ses-03_task-social_acq-mb8*run-03_bold.nii.gz
./sub-0025/ses-03/func/sub-0025_ses-03_task-social_acq-mb8_51_run-03_bold.nii.gz int16 [ 82,  82,  56, 872] 2.68x2.68x2.70x0.46   sform
./sub-0025/ses-03/func/sub-0025_ses-03_task-social_acq-mb8_run-03_bold.nii.gz    int16 [ 82,  82,  56, 275] 2.68x2.68x2.70x0.46   sform

Rename files

code/rename_file --swap --all-extensions ./sub-0025/ses-03/func/sub-0025_ses-03_task-social_acq-mb8{_51,}_run-03_bold.json